This section applies to the ILCOE.
Molzapart is one of the two most powerful legendary Pokémon in the world, along with Chaletwo. He looks like a hybrid of Articuno, Zapdos and Moltres with additional psychic powers, especially various memory modification abilities.
Molzapart was born from an accident: Mew discovered the legendary Mist Stone in Seafoam Islands, rumoured to be able to evolve any Pokémon to a frighteningly powerful form, and called Articuno, Zapdos and Moltres there to help dispose of it, as Mew believed it was dangerous and must be destroyed. However, when their attacks hit it at the same time, the stone managed to morph into an 'evolved form' of their attacks, which turned out to be Molzapart.
Molzapart had a powerful desire to be strong and immediately began to train himself in secret. He grew into the most powerful legendary Pokémon in the world along with Chaletwo, though Chaletwo was of course a true immortal unlike him, and they became acquainted, though they never talked much until they realized around twenty years before the start of the story that their powers were slowly weakening. After talking to Mew and finding out the next War of the Legends was about to happen - Molzapart, like the other legendaries, had not known about the War at all prior to this - they came up with the idea that perhaps the War would not happen if all the legendaries were caught inside Pokéballs at the time it was supposed to start and tried unsuccessfully to convince Mew to participate in this plan. When Mew didn't, they tried the other legendaries, but none of them agreed to it either. Therefore, Chaletwo came up with the idea of recruiting human trainers to the cause to forcibly capture the legendaries.
At first, since Chaletwo was known for just appearing once a year outside Green Town, Molzapart tried to handle the recruiting, but he had a difficult time recruiting people who weren't very reluctant to help out of either lack of ability, fear, faith in Mew or distrust of them. This was compounded by the difficulty of finding people to approach for the cause, though Molzapart did manage to reach Ash Ketchum and convince him to help in an emergency though they knew his involvement would probably bring undesired attention to their attempt. Later Chaletwo took over that aspect and had more success, though Molzapart's memory modification abilities were still essential to the plan.
Molzapart originates from my first ever attempt at fanfiction, Molzapart and Rainteicune.
I was eleven years old. I will not defend him; he was a stupid idea with an even stupider execution and still is. I only wrote him in in the first place because in the original I stuck every bit of a fake legendary anything I had ever made into the book in chapter two, and now here I am, stuck with him in the ILCOE when I'm embarrassed to acknowledge his existence.
My general solution to this dilemma has been to give him as little screentime as possible. In an unannounced revision of the ILCOE, I even took out the paragraph at the end of chapter two that originally explained briefly what Molzapart was (I always meant to add something of an explanation into chapter 20 instead, where he is first mentioned, but I never did, so as it stands Molzapart simply appears out of the blue as if you're supposed to know all about him already, and it mystifies me why so few people have commented on this). Thus, now Molzapart goes completely unmentioned until Alan suddenly talks about him in chapter 20, then suddenly he is one of the two legendaries behind the main plot in chapter 25, then he is briefly mentioned a few times when this is all being explained in chapter 26, then nobody speaks of him again until chapter 39 when Chaletwo finally gives an explanation as to why Molzapart hasn't been babbling in Mark's head all this time like he has, and then they decide to send him with Alan and discuss this somewhat as well as sending him out for a short scene where he knows absolutely nothing of what has been going on since chapter 25. So Molzapart has in the ILCOE so far only had actual dialogue in two chapters and only been briefly mentioned in a few others - he barely even meets the rather loose criteria for getting a character bio at all except for the fact that he is a central part of the main plot of the fic.
The question you should ask, then, is probably, "Then why is he still there?" And there are several answers to that. The first is just the nostalgia factor: while I changed a fair bit of stuff in the ILCOE, all major storyline elements and characters were left alone - this is the same reason as why Mark's Pokémon team remains even though the only one of them that is both a normal, commonish Pokémon and obtained in a non-Sueish way is Sandshrew. While Molzapart wasn't exactly much of a character, I still couldn't just take him out, at least in the ILCOE.
The second is that I need Molzapart's powers in there, specifically the memory modification and Devolution Beam.
The third reason is that Chaletwo needs somebody backing him up. He is not a character that would rise against the world completely alone; he'd first find somebody else to agree with him and then act like he's rising against the world completely alone. Thus, it is essential that some relatively passive character agrees to help him just for the sake of motivating him to do what he does.
That said, in the IALCOTN I am planning to reconsider the Ouenian legendary roster, nostalgia be damned, and neither of the second and third reasons actually requires Molzapart; I just need some legendary with the power to modify memories. Charlie doesn't even need his special ability acquired from Devolution Beam; he never does anything of significance in the fic as anything other than a Charizard. Thus, I plan to finally remove Molzapart in the IALCOTN, probably replacing him with Mementity, a fourth member of the Uxie/Mesprit/Azelf trio who deals with memory and identity.
Nonetheless, I'll still be a bit sad to see him go. His banter with Chaletwo in these two proper chapters he has had was entertaining to write, and I think he'll always have a little place in my heart somewhere in the general vicinity of Faxi the horse*.
*Faxi the horse is the star of the first story I ever actually wrote, when I was seven years old. He had many adventures, such as being almost shot but saved by a tiger, getting a rock stuck in his eye that then fell out, and being on watch while the other horses who had enslaved him slept.