Short Version: Resonance is a Pokémon Fanfic set in the Anime continuity, about a group travelers going back in time to Set Right What Once Went Wrong.
Long Version: In the year 1998 ACnote The year Pokémon Red/Blue was released stateside, the world was ravaged by a horrible virus that turned humans into powerful Pokémon/human hybrids. Ten years later, the last surviving humans struggle for survival, and flee from an enigmatic being known only as the Ivory Queen. Max Maple is one such human, and his life's goal is to get revenge on The Philosophers, an organization of psychics that kidnapped his sister May shortly after the cataclysm. But instead of getting revenge, he ends up joining a man named Oracle on an ambitious quest; to change the future, and prevent the cataclysm from happening. Their destination, 1998, the year a boy name Ash Ketchum begun his Pokémon journey...
It's Personal: His entire motivation for trying to kill Oracle was to rescue May, but it turns out she's too far gone that none of her original personality remains. Not a spoiler, it's all part of the first chapter.
The Musketeer: Subverted. While he owns a Katana, he's terrible at using it. Doesn't hesitate to use his assault rifle, however.
Continuity Snarl: Future!Caitlin uses the same design as the one from Pokémon Black and White, despite the fact that this design has already shown up in the anime. The reason given is that the canon timeline's future!Caitlin also used time travel.
Mid-Season Upgrade: After beating him during the fight club arc, Mao teaches Ash how to perform Magichange.
Swiss Army Superpower: Oracle's recording explains in detail what Ash's powers can actually do, and encourages him to experiment.
Out of Focus: Deconstructed in regards to Ash's Pokémon. Ash relies more on his own powers for protection than his Pokémon, causing him to realize he only has three Pokémon by the time he reaches Vermillion City, and hasn't had a chance to practice battling very much. Luckily for Ash, part of Koga's Training From Hell before the tournament involves going back to catch the Pokémon he missed the first time around.
First Episode Spoiler: Jade kills her early on in the story, inadvertently triggering her elemental powers.
Mega Manning: She can gain new elemental forms by consuming feral elementals.
Mode Lock: While her sisters can transform between human and elemental states, Misty can't return to her a human form. It turns out that this is because she's actually dead, and hasn't realized it yet.
Red Herring: Hints are dropped early on that she could become the Ivory Queen, and later on hints are dropped that she's a Devourer, or at the very least that Elementals inspired legends of the Devourers. Both of these turn out to be untrue, though The Devourers were all once Elementals.
Double Reverse Quadruple Agent: He starts out (supposedly) on N's side, turns out to be working for Ghetsis, but then works with N for real once the stakes are high enough.
Pragmatic Villainy: Points out that people can easily capture and control Pokemon, meaning that Pokemorph super-soldiers wouldn't actually be all that practical.
Well-Intentioned Extremist: Supports Ghetsis over N because he thinks N is too whimsical and unfocused to be the King of Team Plasma. Changes his mind after he realizes that Ghetsis is insane enough to turn his minions into Pokemorph super-soldiers despite protests that it would be a bad idea.
Beauty Is Never Tarnished: Played with. She's never been in a real fight, so of course she doesn't have any battle scars. But even if she did, the technology to remove them exists, and is incredibly cheap at that.
Cosplay Otaku Girl: Likes to dress up in Pokémon costumes and designed Titan's, John's, and Tin's outfits.
Jerk Sue: While she does have her soft spots (her sister and her father, respetively), for the most part she's a jerk to everyone, and this doesn't win her any friends. In fact it actually drives Opal away from her as Jade's hatred for Ash continues to grow. In addition, while she thinks of herself as a strong, independent woman, it's clear that she bases her entire life around others.
A time traveling superhero who went back in time to stop the Ivory Queen from taking over the world. Or not. He actually went back in time to try and make a future where he could be the hero that saved the world instead of Ash. That, and release a virus that would turn everyone into Pokemorphs. The Ivory Queen was just something he made up.
Well-Intentioned Extremist: He plans to release a mutagenic virus that will turn the entire world into Pokemorphs, so that his past self will never feel alone. Unfortunantly, he didn't count on it driving people insane...
A purple-haired prettyboy supervillain sent back in time by the Ivory Queen to destroy the Iron Titan. In reality he's just an actor playing the role of a lifetime. Though he really is a time traveler.
Well-Intentioned Extremist: He kidnapped May and turned her into a living computer in order to amplify her latent psychic powers, allowing him to pinpoint exactly what needs to be changed in order to save the future.
Characters from Fanfic/Morphic
Dogged Nice Guy: Sure, maybe he's not being held hostage by a religious nut who wants to kill him and his family this time around, but he still gets kidnapped by Max, N and Caitlin, gets dragged around all over the planet by said kidnappers, has his life put on the line more times than he can count, and he's really susceptible toTeleportation Sickness.
External Retcon: Issac Danels' motivation for wanting the morphs dead is elaborated upon; according to the church's teachings, the netherworld is ruled by a being called Devourers, humans who consumed the souls of Pokémon to steal their powers. Note that this doesn't attempt to justify Issac's viewpoint, as this would be akin to trying to murder the president because you thought he was the Anticrhist.
The Extremist Was Right: Half-right, anyway. The Devourers exist, and they do rule the netherworld. But none of the Pokémorphs were ever meant to be used as vessels for their rebirth. In fact, in a very, very indirect way, Issac himself ends up being responsible for setting them free.
Jade is represented by Gardevior, an empathetic pokemon who's personality is almost complete opposite of her. In addition, it represents the fusion of human and Pokemon, which is both Titan and Jade's ideal.
Tin's costume resembles Pawniard, which represents his role as a willing lackey to Titan's plan, and his inner moral conflict.
Titan's Powered Armor resembles Zekrom, representing his hope to make the world a better place and his friendship with L.
Tyrian's costume resembles Nidoking, which is a heavy-handed way of showing that he wants to take over the world. Of course the symbolism was entirely deliberate; he doesn't actually want to take over the world, he just wants people to think he does.
Recursive Fanfiction: Though set in the Anime's world, it borrows characters and story elements from Morphic. Of course the author isn't even pretending this is in continuity with Moprhic, and even points out that this story is pretty much it's own canon.
Reimagining The Artifact: Team Rocket being able to recover from their Amusing Injuries is given the justification that all those RPG healing potions you can buy in the games work just as well on humans.
We Will Have Perfect Health in the Future: Used as a plot point: the same medical technology that heals Pokemon injuries also heals humans. Dr. Chandler takes advantage of this technology to create the Pokemorph virus.