This section applies to the ILCOE.
The Quest for the Legends' often slow update speed has an annoying side-effect: when you aren't the author, it can be a little difficult to keep a clear idea of what's going on committed to memory. Hence, this plot recap page will continuously be updated to contain a summary of what's going on as of the start of the latest chapter at any given time. It will not spoil anything that happens in the newest chapter, but if you're more than a single chapter behind, be warned that this page may contain heavy spoilers.
This is not a substitute for reading the fic; it's just a memory refresher. It assumes that you need your memory jogged, not that you just can't be bothered to read sixty-something chapters. Various potential plot holes are explained in the text of the fic but not touched upon here, and subplots that have already been resolved but may be referenced in passing again will be left out completely.
The recap is organized by topic to make it easier to look up any particular details you're fuzzy on.
See the character bios. Spoiler-free backstories are found in the Pre-Story Biography in each character's bio.
The War of the Legends
In the middle of his long-awaited Pokémon journey, Mark Greenlet was killed by the legendary Pokémon Chaletwo. Chaletwo explained to him that he and another legendary, Molzapart, have been recruiting trainers to capture all of the legendary Pokémon in order to prevent a milleniumly phenomenon called 'the War of the Legends', or just 'the War' when the full phrase is too cumbersome. Mark is the latest recruit and the fifth in a row killed by Chaletwo at the Green Town Pokémon Festival, where Chaletwo appears for a few seconds every year.
According to Chaletwo:
The War is caused by a mysterious something called 'the Destroyer', assumed to be a legendary Pokémon. Basically, the Destroyer drains the power of the legendary Pokémon until they are virtually powerless; then, when exactly a thousand years have passed since the beginning of the last War, it releases a pulse of energy that rushes back to the legendaries (distributed evenly between them) and drives them mad. Desperate to release the overwhelming extra energy they've obtained and maddened by the rush of power, the legendaries will brutally fight one another until only one is left alive.
Some residual energy after the carnage settles into the final survivor once all the others are dead. This residual energy has two effects: 1) it makes the recipient a true immortal, meaning that unlike the undying-but-killable normal legendaries, its body cannot be physically destroyed (though the Destroyer will drain its true immortality away along with everything else before the War begins); and 2) it gives it the ability to create life out of inorganic material. Thanks to the latter ability, this Pokémon is referred to as 'the Creator', and it is its responsibility to restore the world to normal and create new legendary Pokémon to watch over it.
The first Pokémon that the Creator creates is also automatically special, thanks to an extra spark of power the Creator has immediately after the War: 1) like the Creator, it is a true immortal, and 2) it automatically has the ability to travel through time. This Pokémon is referred to as 'the Preserver'.
Though obviously this means the Creator and Preserver change after every War, the current Creator (i.e. the survivor of the last War) is Mew, and the current Preserver is Chaletwo himself. Before the last War, according to Mew, the Creator was a bird Pokémon named Iriesce and the Preserver was another legendary Pokémon named Chalenor, who was a friend of Mew's. Chaletwo was created by combining the power from Chalenor's eyes (which, when open, would emit deadly rays towards whatever he looked at) with the body of Mewtwo, who had taken part in the War because Chalenor had traveled to the future and brought Mewtwo back with him shortly before the War.
The hope is that by capturing all of the legendaries, the Destroyer's pulse of energy will not find a target and the War of the Legends will fail to happen, allowing the legendaries to live on for at least another thousand years. However, because Mew had forbidden Molzapart and Chaletwo to tell the other legendaries about the War, fearing chaos would ensue if they were informed of their impending doom, they couldn't convince the other legendaries to willingly let themselves be caught. Turning to humans for help to achieve this was therefore the only option they saw.
Mark agreed to help and was resurrected two weeks after his death. Subsequently he was also joined by May and Alan in his quest, the latter actually because Ash had agreed to help several years earlier if the situation got dire but ultimately it was easier for Alan to go. Chaletwo established a physical anchor to Mark's brain in order to be able to communicate with him, opening himself to having his power drained by the Destroyer in the meanwhile, while Molzapart conserved his powers in a Pokéball in case they were needed (primarily, he has the ability to modify memories). However, later Molzapart linked to Alan as the group split up for the League and is now too weak to perform large-scale memory modification.
Currently, the legendary Pokémon that remain to be caught are Mew, Dracobalt, Venoir, Preciure and the Waraider herd. The group have used up both of their Master Balls. Mark was injured and blacked out while the group were trying to convince Raudra and Puragon to be caught.
The Ouen Legendaries
The Color Dragons are six dragons, all Dragon/Flying-type though four of them specialize in a particular type and can use moves of those types as if they were their own. Three of them - Dragoreen, Raudra and Puragon - are female, while the other three - Preciure, Venoir and Dracobalt - are male. The females had banded together at the Eastern Cliffs; the males might also be together. Since they were children, the males and females have despised one another, and the females (and probably the males as well) are deeply paranoid about their siblings' intentions.
The Waraider Herd is a herd of eight winged unicorns of different types, led by the Normal-type Waraider. It is said that if they are ever separated, the balance of nature will be undone until they are reunited.
The Dragons of Ouen, Thunderyu, Volcaryu and Polaryu, were created and sealed away by Chaletwo when he was young, in an act of youthful rebellion against Mew. They're programmed to each think about nothing but destroying the others. They have all been caught.
Outside Knowledge of the Plan
Sparky, the Gym leader of Stormy Town, is aware that Mark, May and Alan battled an electric dragon (Thunderyu) that was causing the thunderstorms near his town. The cover story they gave him was that it had burst out of the mountain and attacked them, and though he seemed vaguely skeptical, he didn't ask.
Because Volcaryu's awakening would destroy Crater Town, Mark had to call for the town to be evacuated. By chance a woman was reading a two-week-old newspaper and recognized him as the boy who was killed by Chaletwo at the Pokémon Festival, forcing him to make up a story about Chaletwo being evil and intending to take over the world using Volcaryu. Carl, the Gym leader of Crater Town, helped them battle it and then threw the ball that captured it, refusing to give it up afterwards as he wanted to keep it locked away where it could do no more harm. Chaletwo, however, fears Carl will harm Volcaryu.
Mitch, Gym Leader of Scorpio City, knows through his psychic premonitions that Chaletwo chose Mark to help him with something. He also told Victor, who is now assistant Gym Leader of Acaria City. They know nothing else.
Mew also knows of Chaletwo's efforts but disapproves of them, saying that the War is meant to happen. Entei heard about the plan from Chaletwo just before transferring his soul to his soul gem.
Theories on the Destroyer
Mark's first reluctant theory on the Destroyer's identity was that it was Articuno, the second Pokémon created by the Creator after the last War. However, Articuno has been caught by one of the other legendary hunters with no apparent repercussions, ruling this out. Later it occurred to Mark that Mew could be the Destroyer, after being told by Chaletwo that Mew seemed content with the idea of the War and had been reluctant to help with the plan to stop it. However, Chaletwo is confident that Mew can't be the Destroyer, pointing out that Mew chose to tell him, Molzapart and the Beasts of Johto about the War of his own free will, and instead thinks Mew is just tired after living for two full millennia. Instead, Chaletwo believes the Destroyer is some unknown legendary.
The Other Legendary Hunters
Mark and May have met and battled alongside one of Chaletwo's other recruits, Leah Donaldson. She is currently combing the Johto region for Mew, whereas Mary Goldman, another legendary hunter, is heading to Ouen to look for the Waraider herd after successfully capturing Articuno. The locations of Chaletwo's other two legendary hunters are unknown.
Unknown to Chaletwo, the Beasts of Johto - Raikou, Entei and Suicune - have also known about the War for some time and concocted a plan of their own. Rather than try to prevent it altogether, they chose to save themselves using 'soul gems', physical objects (usually gemstones) to which a soul can be anchored to prevent it from disappearing from the world after the death of the body and allow it to be resurrected later. These soul gems would be guarded by a chosen Pokémon.
To ensure that the chosen Pokémon were well-suited to the task, they each picked out several 'potentials' of their own type, lent them a portion of their power - also insuring that power against the Destroyer's power-draining ability - and engineered some tests to put them through, planning to pick one each as their 'Chosen' to carry the soul gems when the time came. They would then transfer their remaining power to the Chosen along with the soul to ensure the Chosen has the best possible ability to defend the gems.
May's Ninetales Spirit and Mark's Gyarados are Entei and Suicune's Chosen respectively, while Raikou was caught by Rick before he could manage to make his final choice.
Rick caught many legendary Pokémon on his journey around the world, and from them he has created a number of low-level clones, kept in specially-modified 'Clone Balls' of his own creation that suppress their free will. He released many of the legendaries he captured again after creating the clones, but others are still held in balls in his Gym and never sent out. The one original he did use was Mew, but Mew fought the influence of the Clone Ball and he ended up giving it to Mark to get rid of it. Mark subsequently switched Mew to a regular Pokéball and released it.
In addition to his straight clones of legendaries, Rick has also been secretly creating genetically modified clones. Most of them are made from regular Pokémon, but he also created "Mewtwo^2", a frighteningly powerful modified Mewtwo. These genetically modified clones are all considerably stronger than the Pokémon they were created from. Rick eventually gave five such super-clones to his brother Taylor, one of them being the aforementioned Mewtwo^2, and Taylor used them to win the Ouen League after using Mewtwo^2 to hypnotize League officials to allow his participation. However, after Taylor's death, his clones were returned to Rick.
Ongoing Subplots, Etc.
All the minor stuff that's really going on at the moment - subplots, arcs, character conflicts, mysteries - ordered by roughly when they were first introduced. Character subplots will assume you know the character's backstory, since that is found in the Pre-Story Biography in their character bios anyway; look there if you've forgotten.
Gyarados and Mark
After killing Suicune at the Lake of Purity only to find out later that Suicune had merely transferred his soul to the soul gems Gyarados himself has engraved into his body, Gyarados's resentment towards legendaries is worse than ever. Mark, however, is finally beginning to sympathize with him upon realizing the legendaries' motives truly were selfish and that Gyarados wasn't actually responsible for Suicune's 'death', and thus he has recently found himself taking Gyarados's side against Chaletwo, especially as Chaletwo fears Gyarados will attempt to destroy Suicune's soul gems.
According to Chaletwo, it is impossible to time-travel to the past: one can only travel to the future and then back to the time where one belongs. While shifted in time, the Destroyer has access to the time-traveler's power through an 'anchor' binding them to their own time. While in the future, the time-traveler must continue to expend energy to maintain the stretch of the anchor, meaning if the Destroyer drained their power until they were too weak to keep themselves there, they would bounce back to their own time automatically. However, this contradicts how Chaletwo was supposedly created, namely from Mewtwo after he had been brought back to before the previous War by the time-traveling Chalenor. Chaletwo theorizes that a time-traveler may be able to bring another being with them to the time-traveler's time, and that some unknown outside force may have kept Mewtwo in Chalenor's time, preventing him from bouncing back as Chalenor's power diminished.
Mewtwo met with the group eventually and explained that Mew had appeared on his island, babbling incoherently about Chalenor, insurance and escaping the War of the Legends, and then created a copy of Mewtwo's body and teleported away. Mark theorizes that this was actually Mew from before the last War, having traveled to the future with Chalenor looking for a way to escape from the War, and one way or another, the copy of Mewtwo's body that he created was what eventually became Chaletwo. Chaletwo protests that this directly contradicts Mew's account of what happened, since Mew explicitly said that Mewtwo had come with Chalenor because he was interested in the past. Mark and May believe that Mew lied to Chaletwo, probably feeling that his own efforts to avoid the War were a horrible mistake and not wanting Chaletwo to know about them, while Chaletwo persists in thinking Mew would have had no reason to lie about these details, and Mewtwo backs him up in saying it sounds unlike Mew. If Chaletwo is right, Chalenor should meet Mewtwo sometime in the future and Mewtwo will go with him to the past; otherwise, Mewtwo will assume Chalenor isn't coming when he is too weak to travel and recall himself into a Pokéball.
Ever since being stung by a Scorplack in the Black Desert when he was young, Mitch has had prescient 'feelings' about things, the ability to teleport, and other strange psychic abilities. These feelings have been intensifying as of late.
After losing to Taylor in the finals of the Ouen League, as even her Tyranitar's heroic efforts were unable to overcome the freakish power possessed by Mewtwo^2, May challenged him to a fairer rematch to set the record straight. When she sent out Tyranitar, however, he fatally attacked Taylor in a misguided attempt to please her by following up on her casual death wishes towards him, and she was forced to release Tyranitar to avoid being connected to Taylor's death.
Upon being informed of his brother's death, Rick's grief, fury and deep-set paranoia caused him to latch wildly on to the idea that someone was at fault, and he agreed to his first ever televised interview, only to use it to deliver incoherent death threats addressed to whomever was responsible for Taylor's murder. Chaletwo has pointed out that Rick has no reason to actually suspect them, but Mark and May are still understandably concerned.
May realized on some level after Taylor's death that Tyranitar's skewed sense of right and wrong was to some degree her own doing. At the Ouen Safari, May caught a Stantler, unusually given it's not a very strong Pokémon. She subsequently made an awkward attempt to imitate how she imagines 'good' trainers are supposed to act towards their Pokémon. However, Stantler called her out on this and proposed that her problem was not that she didn't act enough like a typical 'nice' trainer, but that she'd never bothered to truly get to know her Pokémon in all the time that she'd trained them, and that this had led to her ignorance about both Lapras's distaste for battling and Tyranitar's youth and naivety.