Ash: I want to go back to the day my journey began, when I first set off from Pallet.
Sir Aaron: Hah! Told you, you great lump.
Arceus: I thought 'any day but then' was good odds.
Ash: Were you two betting on me or something?
Sir Aaron: Err… nooo?
Ash: Somehow I don't believe you.
Arceus: Now, Dialga!
Narration: In that second of absolute stillness, Ash thought to himself that using the – a – legendary Pokémon that controlled time to get out of an embarrassing situation really took some beating. Then there was a roar, and he fell into blackness.
Most notable in the case of Ash's Charizard when using Blast Burn. For context, in the games, Frenzy Plant, Hydro Cannon, and Blast Burn are the Grass, Water, and Fire (respectively) versions of Hyper Beam. In this fic, when Ash's Ivysaur and Squirtle use Frenzy Plant and Hydro Cannon, that's how they're portrayed: as powerful but draining finishing attacks. In contrast, Charizard's Blast Burn is second in power only to the Pokemon equivalent of a nuclear warhead.
Similarly, Pikachu's Volt Crash can vaporize a swimming pool in one shot.
Particularly in the case of previously underdeveloped and rather weak Butterfree and Pidgeot.
Alternate Universe: Very subtle, but there are some changes from the main Pokemon universe- and that's not including the changes that the main characters have wrought to the timeline. For example, Hunter J and Lawrence III are brother and sister, and Koga (poison Gym Leader) adopted Meowzie (meaning she left Hollywood, rather than stayed for the episode of the anime where she debuted).
Bag of Holding: Sir Aaron's bag. Lampshaded when Misty boggles at Ash pulling an entire chalkboard out of it. He says the real trick was getting it in there in the first place.
Battle in the Center of the Mind: Used twice so far via Aura Purge. The first time was to help cure Misty's phobia of Bug types by going back to her memory of the traumatic event that caused it and battling a horde of Bugs led by a mental projection of Genesect. That fight was used as a practice run for the battle against Sabrina, which culminated in the only sane fragment of her personality cutting down her inner darkness with a representation of Keldeo's Sacred Sword, Excalibur Galatine.
Berserk Button: For Pidgeot, being mistaken for a male. The first time it happened, she retaliated with a massive Sky Attack and left the message "I'm female, twit" carved into the surface of the glass lining the resulting crater. Subverted the second time, when the culprit managed to apologize for his mistake in time to prevent her wrath.
Curb-Stomp Battle: Due to Ash being able to restore the memories, and power, and evolutionary level, of his Pokémon, and that of his friends, including Jessie, James and Meowth to whatever they were before Cyrus did his thing, they meet some people who they completely overpower.
Early on, when Ash encountered the samurai guy who uses Bug-type Pokémon a second time from his point of view, well, it is easy to guess how that went.
When they did the Princess Tournament again, the early rounds, in the author's words, were one-sided.
Cutting the Knot: With their knowledge of the future, Ash and the other characters are able to avoid a lot of problems with relatively simple solutions. For example, teaming up the man with the Pokeflute that helped them with the Snorlax early in their travels with Jigglypuff, to counteract her sleep-inducing song.
Team Rocket was supposed to do Koga's dungeon of traps before facing him. What instead happened was that they used Abra to teleport directly to Koga at the end of the dungeon.
Discontinuity Nod: Dexter brings up the events of the infamous banned Porygon episode, which none of the others can remember. He attributes the memory loss to seizures brought on by the digital environment.
Ash tends to do this a lot. For example, in one of the Orange League gyms, one of the challenges is a race. While it's implied that you're supposed to use a water type, Ash instead uses his Pidgeot... which is capable of supersonic travel.
Evil Versus Oblivion: The purpose of Rocket executives, or at least the department the promoted Jessie, James, and Meowth are in. You can't rule or make a profit in a destroyed world, so somebody needs to point Idiot Heroes in the right direction to protect all those potential victims.
Field of Bones: Jessie's Cubone (based on Archer) can manifest her reality marble, which takes this form.
Fix Fic: Technically a subversion. Most Fix Fics completely ignore canon after a certain point, but this one only works because the characters have knowledge of canon.
Friendly Enemy: Jessie, James and Meowth. After their memories got restored and Ash explained the situation to them, of course.
Due to Ritchie being "Destiny Entangled" with Ash, he has his own heroic quest to complete... and will face his own world-saving trials.
Some of the Pokemon that Ash lets go have had their own, separate, adventures, and gained unbelievable amounts of power. For example, Butterfree, Lapras, and Pigeot all spent years away from Ash as defenders of their groups or areas.
Hopeless Boss Fight: Ash's Gym Battle against Misty was supposed to be this in order to teach him humility, since in this fic, Gyms are designed to test a Trainer's character as well as their battling prowess. Unfortunately, Ash didn't get the message and ended up accidentally bringing the roof down as a result of his refusal to give up.
Innocent Innuendo: While Jessie and James are challenging Koga at the Fuchsia Gym, Meowth is led away by a female of his species who offers to help "remedy his depression" over feeling worthless as anything other than a translator. The next Jessie and James hear from him, he's crying out ecstatically, which Squicks them out to no end when they realize the implications. Then Meowth walks in and proudly offers to show them why he's so happy now... before demonstrating that the female Meowth has taught him how to finally use Pay Day.
Instant A.I., Just Add Water: Dexter, as well as Gary and Professor Oak's Pokedexes, develop full sentience as a result of uploading all the information Dexter had cataloged from the future and become Porygons.
King of All Cosmos: Arceus and the second Dialga and Palkia, much to Sir Aaron's dismay. "Every hour I'm in here with you guys, my image of the Kami becomes a little more tarnished..."
Ash invokes this when Vulpix turns herself into a Nintetails by remarking that he will make sure to forfeit if Brock gets involved in Pokémon contests.
Laborious Laziness: Abra actually works pretty darn hard at being as lazy as possible. He is capable of teleporting Team Rocket to many places in a very short amount of time, creating shields that are capable of protecting them from Mewtwo, and is able to stand on his own in Pokemon Matches far above his weight class... all in the name of getting a little extra sleep.
Lampshade Hanging: Some of the sillier/weirder/crazier stuff that happened in the anime gets commented on by the characters.
Large Ham: Ash's Squirtle, oh so very much. Same with Gary's Blastoise. Ash has this to say about his Squirtle:
Ash: I've heard of showy, but that turtle takes the cake.
Mewtwo lampshaded it asking if Gary's Blastoise was feeling well.
The Aforementioned Squirtle and Blastoise are massiveGurren Lagann otaku, so it's justified... somewhat.
Magikarp Power: The Trope Namer in action, as this time around, James puts in the effort of actually training the Magikarp he bought from that con artist and ends up with a Gyrados that doesn't just want to blast him into the middle of next month.
Meanwhile, in the Future: The story frequently cuts to the sub-dimensional bubble where Arceus, Sir Aaron, Dialga, and Palkia play lots and lots of board games while waiting for Ash's changes to the timeline to take effect.
Mid-Battle Tea Break: A literal one happens during Ash's gym battle against Erica. Ivysaur and Gloom are locked in a stalemate against each other, easily healing any Scratch Damage the other manages to inflict. During that time, Erica and Misty enjoy a Spot of Tea, a bored Ash starts looking up the record for the longest Pokemon match in history, and both Pokemon resort to using the nearest computer to look up their movesets in search of anything that will turn the tide one way or another.
Mission from God: Arceus himself gave Ash the mission of making sure Cyrus doesn't succeed.
Ritchie is on another one due to his destiny entanglement with Ash.
Mundane Utility: Vulpix uses Safeguard to carry a Fire Stone without triggering her evolution into Ninetails before Brock has properly paid for the Stone.
Mewtwo can use his telekinesis for movie special effects.
Mythology Gag: Arceus creates a second Dialga to send Ash into the past, and later creates a second Palkia to round out his gaming group. In Heart Gold and Soul Silver, Arceus could create a copy of one of the Sinnoh Dragons if brought to the Sinjoh Ruins.
Ash mentions having Dexter develop a way to jailbreak TMs so they could be used more than once while they were in Unova during the original timeline.
James expresses surprise at not whiting out and waking up at the Pokemon Center after running out of usable Pokemon during a battle.
Ash and Gary face each other in the finals of the Indigo League.
Nice Hat: Sir Aaron's hat, which grants its wearer the Dark subtype. This protects Ash from psychic-types and mind reading.
This helps them to get to Shamouti Island the day before they arrived in the previous timeline.
Oh Crap: Ash and Pikachu's reaction to Lt. Surge's Thunderstone accidentally making contact with Pikachu.
A similar reaction happens when Team Ketchum gets blown to Shamouti Island, since they remember full well all the trouble that happened there.
Ooh, Me Accent's Slipping: Yes, even in a fanfiction. The author's British accent accidentally slips through occasionally, such as calling Ho-oh a "Whacking great phoenix," or Ash calling his mother "Mum" when typically he (Ash) speaks with a more North-American version of English.
Pokémon of Mass Destruction: Charizard learned Blast Burn. Also Victini used V-Generate against Hiroshima and Nagasaki in the last World War.
Power Incontinence: While not an overly dangerous version, Mewtwo tends to overwhelm people when he forgets to tone down the natural aura of power he projects. He's quite sorry when he does it unintentionally.
Psychopomp: In this setting, Darkrai is considered the god of death, though he only appears to greet the dead on "special occasions."
Secret Test of Character: Giovanni orders James to give up his beloved Growlie so the Team Rocket highers-up could use his firepower. James ultimately refuses, with Jessie and Meowth backing him up. This convinces Giovanni that the trio have what it takes to be promoted to Executive status and learn about Team Rocket's secondary goal (see Evil Versus Oblivion above).
The Gym matches are revealed to be this- at least partway. Each is designed to teach a different lesson- Brock's is about Endurance, Cerulean's is about not giving in despite hopeless odds, Cinnibar's is about intelligence, the Poison Gym is about tricks...
Ash goes to Cameran to free Aaron's Lucario and collect Aaron's equipment right after getting the Boulder Badge. Compare to the original timeline where he only went to Cameran after the Hoenn League during the Battle Frontier arc.
Ash clashes with Hunter J before he finishes the Kanto League, about the time he was supposed to get Muk. In the original timeline, Ash clashed with Hunter J while in Sinnoh.
Ash captures Muk way later than the original timeline, while helping that movie director, because he forgot about Muk due to the battle with Hunter J.
Sometimes, Ash deliberately uses his knowledge of the future to try to take an "Idealized" path, avoiding trouble spots that he had in the original timeline. For example, his plan for Porta Vista involves grabbing Misty's Horsea and getting out immediately, while his reaction to doing the SS Anne and Maiden's Peak were summed up as "Screw that," and "Not only no, but HELL no" respectively. This allows him and his team far more time to train, and thus get a massive leg up on future problems.
Sneeze Cut: In one chapter, Team Rocket's Meowth went looking around Hollywood for Meowzie, the Meowth that made him want to become human-like, but couldn't find her. We cut to Meowzie sneezing in the Fuchsia Gym, where it had already been established that she was living after Janine had adopted her.
Stating the Simple Solution: Some characters point out to other characters very simple solutions to problems they had during the original timeline. Vague wording due to the fact that the relevant positions are sometimes switched around.
Super Empowering: Ho-Oh grants Togekiss the ability to use Sacred Fire as a birthday gift.
A Running Gag throughout the fic is how just being around Ash seems to trigger evolution in other people's Pokemon, even the ones he can't restore to the way they were at the end of the former timeline.
At one point, Professor Oak tries to justify it as the fact that Ash gives off so much Aura that exposed Pokemon are given a massive power boost and can evolve much more easily that way. Ash rejects this, as even before he got a massive Aura power boost, pokemon would still spontaneously evolve around him (such as Caterpie, Ponyta, and Charmander (for a very abridged list of all the evolutions that happen around him)).
Weather Dissonance: The crazy weather Ash and the others have to put up with on occasion is implied to be a result of Butterfree disrupting the weather patterns when he used Sunny Day in the middle of a rainstorm to save Charmander's life. Another possibility that gets suggested is that temperamental Legendaries are to blame. Given that some of the legendaries are genuinely insane (as shown in the segments with Aaron), this is entirely possible.
Mewtwo causes a massive storm that threatens to wipe out humanity, but that was already canon.
It's bad enough that in Chapter 38 (as of this edit the most recent chapter), Misty resolves an issue that originally took an entire episode without violence in a few minutes. Ash dives for cover, and even when he gets out he still prepares for an airship crash or Legendary encounter or suchlike. Considering the chapter ends at Shamouti, which had both happen...
What the Hell, Hero?: When facing the Grass Gym, Ash temporarily forgets that he has Charizard. The strongest fire pokemon on his team. Who he specifically brought for this gym. Who has Blast Burn, an attack that is only second in power to the local equivalent of a nuclear strike. Ivysaur, who had just gotten done with what is lampshaded as one of the longest pokemon matches ever (due to various moves not effecting the combatants), was not pleased at this little fact, and roughs up Ash appropriately.
Wrong Genre Savvy: Played doubly straight with Lt. Surge, who initially believes Riolu's Aura Sphere is a close-range attack because of an anime he watched, resulting in his Pokemon getting knocked out. However, he later shows that his knowledge of Electric Type Pokemon is top notch when his Raichu overloads Pikachu, something even Ash wasn't aware could happen.
You're Insane!: Aaron's reaction to the concept of a "Legendary Pokemon Three Legged Race," especially since there are so many variations on how pokemon move- ranging from hovering (no legs) to having too many legs for the race to work, not to mention the sheer difference in sizes between them. Arceus admits that the whole idea was because he was running out of games.