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A tl;dr walkthrough of Martel's very undetailed canon history
In the ancient past of a world that may have been named Aselia before, they've never actually said, the elves descended from the comet-world of Derris-Kharlan, and brought the Giant Kharlan Tree, which provided the world with with the incredible life-sustaining power of mana. Therefore this brought life to the planet, including humans.
This also brought half-elves, because apparently some of the humans and elves found each other very doable. The only confirmed human/elf couples we know of involved a human man and elven woman, so it's unclear if the reverse is also possible. Half-elves are capable of having children themselves, for the record. The elves didn't like the half-elves because they were part human, and the humans didn't like half-elves because of their longer lifespans and magic powers. This often even included the ones who were hooking up interracially. So, as racism likes to go, the half-elves had already been horribly persecuted for over a thousand years where Martel's story begins.
Martel Yggdrasill was born and raised in Heimdall, the isolated sole village of elves that had remained on the planet. She was a half-elf herself, but the identities of her parents and why they were allowed to make their lives there has never been expounded upon. Roughly ten years later, her younger brother Mithos was born.
Meanwhile, people had been using mana to power incredible technology (called magitechnology), and had realized that the mana from the Giant Kharlan Tree was not a quickly renewable resource. Seeing as mana was providing life to the world, this was a problem. The nations of Sylvarant and Tethe'alla had spent a thousand years quarreling over it, and now they finally started an all-out war for the remaining mana, meanwhile making even more powerful technology to fight said war and sapping the tree further.
As this conflict broke out, something bad happened in Heimdall. We have no details about what, but evidently it did transpire because they found some excuse to blame it on half-elves and Martel and Mithos were banished from the village. How old they were and what happened to their parents is also entirely unmentioned. We DO know that by now, Martel was responsible for the brunt of raising her brother.
Heimdall was in Tethe'allan territory, so they started trying to survive there. It was hard because the humans were just as oppressive against half-elves. Martel and Mithos learned how to fend for themselves, including how to make medicines from plants and the like. They were able to earn money through their great skill with gambling, although whether this is learned or pure luck isn't clear. They still couldn't settle down comfortably anywhere for long due to the racism.
Somehow, though, the Yggdrasills stayed very idealistic. They believed there was a peaceful solution to the mana supply problem out there, because at this rate the planet would die, and dreamed of seeing a world where all races could live together in harmony. They decided to work toward that goal together. Of course, this was hindered by their needing to first and foremost survive.
When Mithos was 13 or 14, he and Martel caught wind of the fact that one of the captains in Sylvarant's military was a half-elf. They made their way to the other nation, hoping that this was a sign of better treatment. This was not to be, however. Half-elves were practically regarded as slaves there (how the captain thing happened they haven't said), and it was actually less bad for them in Tethe'alla.
The journey was not a wasted effort however, because somehow they learned of a devastating attack Sylvarant was planning against Tethe'alla's capitol. They hurried to that city to try and warn them, but found it very difficult to get people to listen because they were half-elves. One human knight captain named Kratos was willing to take them seriously and managed to get all of them an audience with the king. But all this got them was Kratos being ridiculed for listening to half-elves and he was driven from the military. Fortunately Kratos was a pretty cool guy who realized that if his country's leaders were going to be like that, they weren't worth it, and he also agreed to tutor Mithos in swordsmanship, as Martel was strictly a mage.
Despite that whole mess, they still sought to stop the attack against Tethe'alla's capitol. With his old military ties probably, Kratos managed to arrange a meetup with the half-elf captain from Sylvarant, a guy named Yuan. All we know about this meeting is that Yuan left after hearing them out and it didn't stop the assault. Martel and the others had returned to the capitol in time for this, probably still trying to prevent it. As it burned before them and Mithos despaired over where they could live, she saw that he had the potential for great darkness were he to really snap for some reason. Although that was not the case this time, she did not forget this.
Ever the optimists, the Yggdrasills still wanted to end the war as peacefully as possible. They were rejoined by Yuan, who had been banished by Sylvarant for some unknown reason, and he proclaimed that he was going with them to prove they were hypocrites about all of this.
Here's where the timeline gets really vague! The timeframe before the next bit of official canon would have definitely included all four of them ending up with Hi-Exspheres with Key Crests which allowed them to become angels, but whether this was all at the same time or not is not addressed at all. The transformation had its negative side effects, but otherwise it gave them additional strength, magic, and shiny mana wings they could make appear at will and fly with. Apparently they had to use a lot of discretion in doing so, however. Also Yuan started agreeing with their outlook but was too stubborn to admit it, which made it especially awkward when at some point he started crushing on Martel like a lovesick middle schooler. She did not seem to notice even though everyone else did, although honestly I've started thinking she actually would have known from something she said in Rays, but blah blah headcanon I can't prove because it wasn't specifically said about this blah.
Definitely after both of those had happened, they were in the area of the town Ozette while a nasty flu was going around. Martel and Mithos wanted to try to help heal the sick, but they were not welcomed in town for long. Outside, they decided to search for fandalia flowers with which they could make medicine, and then have Kratos deliver it so the humans would actually accept it. Martel conveniently failed to mention that she wasn't feeling well, and it was only when she collapsed after the plants had been located that they discovered she had come down with the flu due to her previous contact with the sick. The medicine worked, however, and she was cured.
Several other things happened sometime during these travels, as well. Mithos at some point in his life learned the art of forming pacts with the Summon Spirits of the world, and they traveled to the temples and their other locations so he could gain the help of all of them. He promised that he was going to use their strength to help end the war and save the world. Most notable was the pact with Origin, with which Mithos created the Eternal Sword which could make almost anything possible. More on that later. Also, they went to the Giant Kharlan Tree at least once and met its spirit Ratatosk. And they gained their fifth "companion" when Kratos saved the Protozoan, Noishe.
Martel developed Chronic Angelus Crystallus Inofficium at some point too and likely hid it from the others until they found out somehow. I'm guessing that dress and all its openings on bare skin. Anyway, this was a rare condition caused by her body rejecting her Hi-Exsphere that was starting to gradually and painfully crystallize her whole body. The medical knowledge about this during the era is unclear, but somehow they became aware that once her skin was completely crystallized it would move to her organs and would eventually kill her if not cured. It was a rare enough illness that there were no treatments.
Martel reached a point where she was just ready to accept her fate and die from it, which is when Yuan swore to protect her and proposed. This probably means their relationship had turned romantic at some point before this, but it's Yuan and it's Martel; that could be a completely wrong assumption. Anyway, she accepted the engagement ring and it seems like this got her willing to fight again. Through who knows how much research (since limited amounts were retained for the future), they figured out the cure. The ingredients were acquired although it's not known how difficult that process was either, and they managed to get the Rune Crest made to heal her of this too.
Oddly enough, there's one thing we've seen that technically wasn't canon, although I suspect it eventually happened at a different point than the Ozette flu situation which is why it's being mentioned. Martel spoke to Kratos about her worries regarding Mithos, what with him nearly falling apart after Tethe'alla's capitol was lost and the fact that he never really got to spend time with people his own age. She asked Kratos to watch over him too.
After all of that (though possibly not her Chronic Angelus Crystallus Inofficium ordeal, it's that vague), the four of them managed to bring the war to an end somehow and were regarded as heroes. They got the leaders to sign peace treaties and everything! All was not quite solved, however. The use of mana during the war had all but finished off the Giant Kharlan Tree. All that remained was called the Great Seed, because like a plant, it still had a chance to grow. Derris-Kharlan was approaching the planet again on one of its hundred-year cycles, and being the source of mana, it could restore the Kharlan Tree and save the world. In order to keep the Great Seed from running out of mana before Derris-Kharlan could get there, Mithos used the Eternal Sword to split the world into two that existed on different planes because somehow that used less mana, and they could wait "some decades" until the comet got there and saved the world.
This happy resolution was not to be, sadly. A human only identified as someone the four heroes had previously been allied with at one point decided to try to monopolize the mana just as Derris-Kharlan was going to arrive. He or she was willing to fight to this end, apparently revealing a racial bias against half-elves as well. Martel was still weak from her fighting against her illness (so that may have happened late in their story), and in her nature of putting others' well-being before her own, she was fatally wounded by this person after jumping in their way while defending the Great Seed. She didn't live much longer, but at least had time to express her wish to see a world free from discrimination before she died.
That's when things really started to go downhill for her. For one, when an Exsphere is attached to someone, it gradually absorbs the person's very being into it. Basically this means that although they can die, their consciousness will go on as long as the Exsphere exists with little to no way of interacting with anything. This was apparently fairly well-known then, given what happened next.
Losing the primary guiding force in his life was the breaking point for Mithos. He abandoned their plans for saving the world, and instead fused Martel's Exsphere with the Great Seed to keep her existence from fading away. He also used the Eternal Sword to fix Derris-Kharlan over the world, which would continue to provide them with enough mana to keep up the Great Seed. Because she was able to see and hear everything from her location in the seed, Martel was at least basically aware of what transpired after this, especially Mithos' plans and actions.
With the support of Kratos and to a lesser extent Yuan, Mithos formulated a vast conspiracy over the years so he could reunite with Martel. The countries were to remain as two separate worlds to better control the mana flow. On top of that, he came up with a system where one world would get more mana than the other for a while and then trade off to prevent people from developing the same technologies that nearly destroyed the world before.
By "a while", I mean a few hundred years. It's unclear when they first learned or why they implemented this even before Martel died, but one technique developed by angels during the war allowed them to slow their metabolism nearly to a halt. Consistently using this could keep one alive far past even the average thousand-year lifespan of an elf or half-elf. The three remaining heroes made use of this to carry out Mithos' new plan.
Bringing Martel back to life was going to take several things, one of which was an incredible amount of mana. In fact, it would use up the Great Seed were he to succeed and destroy the world, which did not worry him as much as it might have with Derris-Kharlan around to live on. Most of the Summon Spirits were split between the two worlds to protect the Great Seed and keep it from growing again what with the mana source stuck there.
She also would need a new body to inhabit, and that proved to be the trickiest of all. A near-exact match to Martel's own mana signature would have to be found in someone, and then they would have to be made an angel and sacrifice their own conscious for her to take over. To speed this along, Mithos started a selective breeding program among humans, whom he now loathed and blamed for Martel's death. To keep people from questioning the setup, a religious organization called Cruxis was established under the guise that Martel had been a goddess and Mithos a human hero who had sacrificed himself to save the world's mana. While one world was getting less of the mana flow, they were told that the world was "declining" and the next woman in the Chosen One breeding line went on a journey at age 16 to "restore it", but really it was just to turn her into a suitable vessel for Martel. The journey had to be dangerous to work, and many Chosens died in the process. Whenever one made it to the end, they would lose their own consciousness and try to get Martel's soul fused into them, though this always ended in failure. Mithos would switch the mana flow to be stronger in that world regardless, and the other became the one in decline. The now prospering world would continue the human breeding line, and allowed men born into it to take the Chosen One title as they would not be going on journeys to become Martel's body.
This was taking centuries, and their supply of Exspheres needed to last. To maintain the supply, Mithos eventually allowed half-elves in the declining world to run Human Ranches. Yes, it's as bad as it sounds. They would imprison humans and force them to wear Exspheres to power them up with their life forces. Experiments were also run in both worlds when they began to run low on Hi-Exspheres, or Cruxis Crystals as they were now called, which were required for anyone to make the transition to an angel.
Then there was the issue of the discrimination-free world Martel had wished to see. Mithos decided that if everyone had inorganic bodies and no free will, race wouldn't matter! So his plans also included working toward an Age of Lifeless Beings. As he was otherwise stuck in his 14-year-old body, he made an adult form for himself inorganically to better appear as the leader of Cruxis. There was also an inorganic body made for Martel which she wouldn't inhabit either, but apparently this was Kratos' idea and she ended up being the automated doll Tabatha after that failure.
As previously mentioned, Martel at least knew the gist of what was going on. The Great Seed was in a large chamber that Mithos probably used a lot and presumably talked to her about everything he was doing to "help" and other goings on. She could never say or do anything to protest his actions, as she would never choose her own existence over that of the world.
This went on for four thousand years. Yuan, who was always aware that all of this was against Martel's wishes, had been running an underground resistance group for the last several centuries of this time. Kratos only realized that the Mithos he knew in the past was long gone a few decades before the main canon events took place, tried to hide out for a while and even started a family, but after they were killed he lost his will to oppose Mithos' plans and went back to helping.
Perhaps I should have said Kratos thought his whole family was killed because, as fate would have it, his son survived with Noishe in Sylvarant and ended up being raised in the same area as the Chosen who was going to be the best mana match to Martel yet. And they were at worst besties depending on your relationship choices in the game. So even though Colette, the aforementioned Chosen One, completed her journey, she managed to survive thanks to Lloyd, who was just as much of an idealist as Mithos once was.
Lloyd had met a summoner from Tethe'alla named Sheena and had started forming new pacts with the Summon Spirits, as Mithos had broken his vows and rendered them void should someone come to make a new pact. Yuan thought they should acquire all eight of the ones being used to seal the Great Seed, because as the Yggdrasills' previous plan went, it just needed mana from Derris-Kharlan to germinate it and be restored. Martel's existence would be lost in the process, but he rightly assumed that was more preferable to her than the "everyone dies" option. Unfortunately, dealing with the Great Seed was way more complicated than that and if I understood why, I would explain it. What matters is it went out of control in Sylvarant and wreaked havoc in a large city. With her soul bound to it, this meant Martel's mana was going out of control as well. They restrained it with a mana blast, but this led to the first noise she'd made in millennia, particularly a scream heard 'round the worlds.
Mithos was not giving up in spite of the growing opposition, and eventually captured Colette and forced Martel's soul into her. Finally she could communicate, and she told him that everything he'd done was wrong. Martel begged him to stop all of this and remember the world they had actually wanted. She willingly left Colette to return to the Great Seed once a Key Crest made it possible, but not before commenting that maybe things would have been better if half-elves like them had never been born.
But she phrased that horribly depressing statement in such a way that Mithos decided she couldn't possibly have rejected him like everyone else had already and she meant she just wanted to live on Derris-Kharlan the whole time, so he began to sever its tie to the worlds. Without that mana or the Great Seed, they were still doomed.
And that's her canon point.
... =D
This also brought half-elves, because apparently some of the humans and elves found each other very doable. The only confirmed human/elf couples we know of involved a human man and elven woman, so it's unclear if the reverse is also possible. Half-elves are capable of having children themselves, for the record. The elves didn't like the half-elves because they were part human, and the humans didn't like half-elves because of their longer lifespans and magic powers. This often even included the ones who were hooking up interracially. So, as racism likes to go, the half-elves had already been horribly persecuted for over a thousand years where Martel's story begins.
Martel Yggdrasill was born and raised in Heimdall, the isolated sole village of elves that had remained on the planet. She was a half-elf herself, but the identities of her parents and why they were allowed to make their lives there has never been expounded upon. Roughly ten years later, her younger brother Mithos was born.
Meanwhile, people had been using mana to power incredible technology (called magitechnology), and had realized that the mana from the Giant Kharlan Tree was not a quickly renewable resource. Seeing as mana was providing life to the world, this was a problem. The nations of Sylvarant and Tethe'alla had spent a thousand years quarreling over it, and now they finally started an all-out war for the remaining mana, meanwhile making even more powerful technology to fight said war and sapping the tree further.
As this conflict broke out, something bad happened in Heimdall. We have no details about what, but evidently it did transpire because they found some excuse to blame it on half-elves and Martel and Mithos were banished from the village. How old they were and what happened to their parents is also entirely unmentioned. We DO know that by now, Martel was responsible for the brunt of raising her brother.
Heimdall was in Tethe'allan territory, so they started trying to survive there. It was hard because the humans were just as oppressive against half-elves. Martel and Mithos learned how to fend for themselves, including how to make medicines from plants and the like. They were able to earn money through their great skill with gambling, although whether this is learned or pure luck isn't clear. They still couldn't settle down comfortably anywhere for long due to the racism.
Somehow, though, the Yggdrasills stayed very idealistic. They believed there was a peaceful solution to the mana supply problem out there, because at this rate the planet would die, and dreamed of seeing a world where all races could live together in harmony. They decided to work toward that goal together. Of course, this was hindered by their needing to first and foremost survive.
When Mithos was 13 or 14, he and Martel caught wind of the fact that one of the captains in Sylvarant's military was a half-elf. They made their way to the other nation, hoping that this was a sign of better treatment. This was not to be, however. Half-elves were practically regarded as slaves there (how the captain thing happened they haven't said), and it was actually less bad for them in Tethe'alla.
The journey was not a wasted effort however, because somehow they learned of a devastating attack Sylvarant was planning against Tethe'alla's capitol. They hurried to that city to try and warn them, but found it very difficult to get people to listen because they were half-elves. One human knight captain named Kratos was willing to take them seriously and managed to get all of them an audience with the king. But all this got them was Kratos being ridiculed for listening to half-elves and he was driven from the military. Fortunately Kratos was a pretty cool guy who realized that if his country's leaders were going to be like that, they weren't worth it, and he also agreed to tutor Mithos in swordsmanship, as Martel was strictly a mage.
Despite that whole mess, they still sought to stop the attack against Tethe'alla's capitol. With his old military ties probably, Kratos managed to arrange a meetup with the half-elf captain from Sylvarant, a guy named Yuan. All we know about this meeting is that Yuan left after hearing them out and it didn't stop the assault. Martel and the others had returned to the capitol in time for this, probably still trying to prevent it. As it burned before them and Mithos despaired over where they could live, she saw that he had the potential for great darkness were he to really snap for some reason. Although that was not the case this time, she did not forget this.
Ever the optimists, the Yggdrasills still wanted to end the war as peacefully as possible. They were rejoined by Yuan, who had been banished by Sylvarant for some unknown reason, and he proclaimed that he was going with them to prove they were hypocrites about all of this.
Here's where the timeline gets really vague! The timeframe before the next bit of official canon would have definitely included all four of them ending up with Hi-Exspheres with Key Crests which allowed them to become angels, but whether this was all at the same time or not is not addressed at all. The transformation had its negative side effects, but otherwise it gave them additional strength, magic, and shiny mana wings they could make appear at will and fly with. Apparently they had to use a lot of discretion in doing so, however. Also Yuan started agreeing with their outlook but was too stubborn to admit it, which made it especially awkward when at some point he started crushing on Martel like a lovesick middle schooler. She did not seem to notice even though everyone else did, although honestly I've started thinking she actually would have known from something she said in Rays, but blah blah headcanon I can't prove because it wasn't specifically said about this blah.
Definitely after both of those had happened, they were in the area of the town Ozette while a nasty flu was going around. Martel and Mithos wanted to try to help heal the sick, but they were not welcomed in town for long. Outside, they decided to search for fandalia flowers with which they could make medicine, and then have Kratos deliver it so the humans would actually accept it. Martel conveniently failed to mention that she wasn't feeling well, and it was only when she collapsed after the plants had been located that they discovered she had come down with the flu due to her previous contact with the sick. The medicine worked, however, and she was cured.
Several other things happened sometime during these travels, as well. Mithos at some point in his life learned the art of forming pacts with the Summon Spirits of the world, and they traveled to the temples and their other locations so he could gain the help of all of them. He promised that he was going to use their strength to help end the war and save the world. Most notable was the pact with Origin, with which Mithos created the Eternal Sword which could make almost anything possible. More on that later. Also, they went to the Giant Kharlan Tree at least once and met its spirit Ratatosk. And they gained their fifth "companion" when Kratos saved the Protozoan, Noishe.
Martel developed Chronic Angelus Crystallus Inofficium at some point too and likely hid it from the others until they found out somehow. I'm guessing that dress and all its openings on bare skin. Anyway, this was a rare condition caused by her body rejecting her Hi-Exsphere that was starting to gradually and painfully crystallize her whole body. The medical knowledge about this during the era is unclear, but somehow they became aware that once her skin was completely crystallized it would move to her organs and would eventually kill her if not cured. It was a rare enough illness that there were no treatments.
Martel reached a point where she was just ready to accept her fate and die from it, which is when Yuan swore to protect her and proposed. This probably means their relationship had turned romantic at some point before this, but it's Yuan and it's Martel; that could be a completely wrong assumption. Anyway, she accepted the engagement ring and it seems like this got her willing to fight again. Through who knows how much research (since limited amounts were retained for the future), they figured out the cure. The ingredients were acquired although it's not known how difficult that process was either, and they managed to get the Rune Crest made to heal her of this too.
Oddly enough, there's one thing we've seen that technically wasn't canon, although I suspect it eventually happened at a different point than the Ozette flu situation which is why it's being mentioned. Martel spoke to Kratos about her worries regarding Mithos, what with him nearly falling apart after Tethe'alla's capitol was lost and the fact that he never really got to spend time with people his own age. She asked Kratos to watch over him too.
After all of that (though possibly not her Chronic Angelus Crystallus Inofficium ordeal, it's that vague), the four of them managed to bring the war to an end somehow and were regarded as heroes. They got the leaders to sign peace treaties and everything! All was not quite solved, however. The use of mana during the war had all but finished off the Giant Kharlan Tree. All that remained was called the Great Seed, because like a plant, it still had a chance to grow. Derris-Kharlan was approaching the planet again on one of its hundred-year cycles, and being the source of mana, it could restore the Kharlan Tree and save the world. In order to keep the Great Seed from running out of mana before Derris-Kharlan could get there, Mithos used the Eternal Sword to split the world into two that existed on different planes because somehow that used less mana, and they could wait "some decades" until the comet got there and saved the world.
This happy resolution was not to be, sadly. A human only identified as someone the four heroes had previously been allied with at one point decided to try to monopolize the mana just as Derris-Kharlan was going to arrive. He or she was willing to fight to this end, apparently revealing a racial bias against half-elves as well. Martel was still weak from her fighting against her illness (so that may have happened late in their story), and in her nature of putting others' well-being before her own, she was fatally wounded by this person after jumping in their way while defending the Great Seed. She didn't live much longer, but at least had time to express her wish to see a world free from discrimination before she died.
That's when things really started to go downhill for her. For one, when an Exsphere is attached to someone, it gradually absorbs the person's very being into it. Basically this means that although they can die, their consciousness will go on as long as the Exsphere exists with little to no way of interacting with anything. This was apparently fairly well-known then, given what happened next.
Losing the primary guiding force in his life was the breaking point for Mithos. He abandoned their plans for saving the world, and instead fused Martel's Exsphere with the Great Seed to keep her existence from fading away. He also used the Eternal Sword to fix Derris-Kharlan over the world, which would continue to provide them with enough mana to keep up the Great Seed. Because she was able to see and hear everything from her location in the seed, Martel was at least basically aware of what transpired after this, especially Mithos' plans and actions.
With the support of Kratos and to a lesser extent Yuan, Mithos formulated a vast conspiracy over the years so he could reunite with Martel. The countries were to remain as two separate worlds to better control the mana flow. On top of that, he came up with a system where one world would get more mana than the other for a while and then trade off to prevent people from developing the same technologies that nearly destroyed the world before.
By "a while", I mean a few hundred years. It's unclear when they first learned or why they implemented this even before Martel died, but one technique developed by angels during the war allowed them to slow their metabolism nearly to a halt. Consistently using this could keep one alive far past even the average thousand-year lifespan of an elf or half-elf. The three remaining heroes made use of this to carry out Mithos' new plan.
Bringing Martel back to life was going to take several things, one of which was an incredible amount of mana. In fact, it would use up the Great Seed were he to succeed and destroy the world, which did not worry him as much as it might have with Derris-Kharlan around to live on. Most of the Summon Spirits were split between the two worlds to protect the Great Seed and keep it from growing again what with the mana source stuck there.
She also would need a new body to inhabit, and that proved to be the trickiest of all. A near-exact match to Martel's own mana signature would have to be found in someone, and then they would have to be made an angel and sacrifice their own conscious for her to take over. To speed this along, Mithos started a selective breeding program among humans, whom he now loathed and blamed for Martel's death. To keep people from questioning the setup, a religious organization called Cruxis was established under the guise that Martel had been a goddess and Mithos a human hero who had sacrificed himself to save the world's mana. While one world was getting less of the mana flow, they were told that the world was "declining" and the next woman in the Chosen One breeding line went on a journey at age 16 to "restore it", but really it was just to turn her into a suitable vessel for Martel. The journey had to be dangerous to work, and many Chosens died in the process. Whenever one made it to the end, they would lose their own consciousness and try to get Martel's soul fused into them, though this always ended in failure. Mithos would switch the mana flow to be stronger in that world regardless, and the other became the one in decline. The now prospering world would continue the human breeding line, and allowed men born into it to take the Chosen One title as they would not be going on journeys to become Martel's body.
This was taking centuries, and their supply of Exspheres needed to last. To maintain the supply, Mithos eventually allowed half-elves in the declining world to run Human Ranches. Yes, it's as bad as it sounds. They would imprison humans and force them to wear Exspheres to power them up with their life forces. Experiments were also run in both worlds when they began to run low on Hi-Exspheres, or Cruxis Crystals as they were now called, which were required for anyone to make the transition to an angel.
Then there was the issue of the discrimination-free world Martel had wished to see. Mithos decided that if everyone had inorganic bodies and no free will, race wouldn't matter! So his plans also included working toward an Age of Lifeless Beings. As he was otherwise stuck in his 14-year-old body, he made an adult form for himself inorganically to better appear as the leader of Cruxis. There was also an inorganic body made for Martel which she wouldn't inhabit either, but apparently this was Kratos' idea and she ended up being the automated doll Tabatha after that failure.
As previously mentioned, Martel at least knew the gist of what was going on. The Great Seed was in a large chamber that Mithos probably used a lot and presumably talked to her about everything he was doing to "help" and other goings on. She could never say or do anything to protest his actions, as she would never choose her own existence over that of the world.
This went on for four thousand years. Yuan, who was always aware that all of this was against Martel's wishes, had been running an underground resistance group for the last several centuries of this time. Kratos only realized that the Mithos he knew in the past was long gone a few decades before the main canon events took place, tried to hide out for a while and even started a family, but after they were killed he lost his will to oppose Mithos' plans and went back to helping.
Perhaps I should have said Kratos thought his whole family was killed because, as fate would have it, his son survived with Noishe in Sylvarant and ended up being raised in the same area as the Chosen who was going to be the best mana match to Martel yet. And they were at worst besties depending on your relationship choices in the game. So even though Colette, the aforementioned Chosen One, completed her journey, she managed to survive thanks to Lloyd, who was just as much of an idealist as Mithos once was.
Lloyd had met a summoner from Tethe'alla named Sheena and had started forming new pacts with the Summon Spirits, as Mithos had broken his vows and rendered them void should someone come to make a new pact. Yuan thought they should acquire all eight of the ones being used to seal the Great Seed, because as the Yggdrasills' previous plan went, it just needed mana from Derris-Kharlan to germinate it and be restored. Martel's existence would be lost in the process, but he rightly assumed that was more preferable to her than the "everyone dies" option. Unfortunately, dealing with the Great Seed was way more complicated than that and if I understood why, I would explain it. What matters is it went out of control in Sylvarant and wreaked havoc in a large city. With her soul bound to it, this meant Martel's mana was going out of control as well. They restrained it with a mana blast, but this led to the first noise she'd made in millennia, particularly a scream heard 'round the worlds.
Mithos was not giving up in spite of the growing opposition, and eventually captured Colette and forced Martel's soul into her. Finally she could communicate, and she told him that everything he'd done was wrong. Martel begged him to stop all of this and remember the world they had actually wanted. She willingly left Colette to return to the Great Seed once a Key Crest made it possible, but not before commenting that maybe things would have been better if half-elves like them had never been born.
But she phrased that horribly depressing statement in such a way that Mithos decided she couldn't possibly have rejected him like everyone else had already and she meant she just wanted to live on Derris-Kharlan the whole time, so he began to sever its tie to the worlds. Without that mana or the Great Seed, they were still doomed.
And that's her canon point.
... =D