During the opening ceremonies of the Indigo League, Moltres itself shows up and lights the torch.
Who are we kidding; the whole premise is one!
Ash's Squirtle is a walking, talking, Tengen Toppa Gurren Lagann reference. Worse? He's memetic. Gary is initially angry that Ash's Squirtle turned his Squirtle into post-time-skip Simon (not literally).
Just seeing Ash going mano-a-mano against Pokemon on his own is one.
Even if he lost, Ash did put up a pretty good fight against Lorelei, who in canon beat him up, down and sideways without much effort. This time, Ash managed to bring Lorelei down to her last Pokemon and only lost because Jynx's Focus Sash allowed her to barely endure Tauros' Fissure.
A slight one for the author by managing to get a pretty accurate guess on how Keldeo would be depicted well before his featured movie was released.
Ash giving Mewtwo a run for his money in one-on-one combat.
The way he does it is awesome too. Ash needs to use Ghost type moves to do any damage to Mewtwo, a Psychic type, and he figures out how to do that. How? His own blood. And by the end, he was almost out of it, and nearly died from blood loss. Ash was fully prepared to put his life on the damn line and possibly die to knock some sense into Mewtwo.
He actually did die, but the Sacred Ash brought him back. Doesn't diminish the awesome, though.
Same chapter: thanks to the storm and the fight coming too close to the sea, J's Salamence manages to reverse the course of the fight and gain the upper hand on Charizard. Cue Squirtle stopping him. He then tricks the Salamence into the path of Articuno's Aurora Beam, making the poor dragon part of the collateral damage of the three-way battle battle between Articuno, Zapdos and Moltres.
Still, it's three Olympus Mons we're talking about, they don't go down easy. So in the following chapter Charizard and Pidgeot start fighting Articuno and Moltres, and give them a desperate run for their money. And Charizard is already tired from the battle with Salamence. And yet, they hold long enough for Lugia to get the drop on them and give them the well-deserved thrashing he had wanted to give them and Zapdos for a long time.
And how do you top the above? When Charizard gets too tired to continue fighting, the real Legendary Beasts show up. And, being used to work like a group, start dishing an even worse beating on their opponents.
When the Unown are close to go critical like in the movie, Brock stops it with a swing of his crowbar.
And, Mewtwo being Mewtwo, he also recovered Molly's parents and took the chance to make the illusionary Beasts and the illusionary Eevee real. And (accidentally) Shiny. Oh, and the Eevee can evolve and de-evolve at will.
The battle with Whitney. Who confirms herself as That One Boss with: a Clefairy that nearly defeated Totodile before two unlucky Metronomes cured the Water-type and self-destructed the Normal-type; an idiotic Bidoof that proves himself much stronger than he's intelligent; and the goddamn' Miltankfrom hell. Then Muk shows up and overpowers Miltank, and by overpowers we mean unleashes no less than 20 different attacks all at once.
Here is the list: Thunderbolt, Flamethrower, Shadow Ball, Rock Tomb, Shock Wave, Fire Blast, Focus Blast, Secret Power, Dark Pulse, Sludge Bomb, Giga Drain, Hyper Beam, Ice Punch, Hidden Power, Double Team, Round, Payback, Rain Dance, Sunny Day and Toxic
In chapter 64, Pidgeot too Mega-Evolves. Again, without stones.
Chapter 65 features Keldeo showing why he's one of the Swords of Justice.
In chapter 67, Misty receives a letter. It's a notice that she's being scouted as a possible member of the Elite 4.
Houndour first gym battle against Morty's Gengar. He wins. Especially notable the Beat-Up attack (a move in which doubles of all of Ash's Pokemon on hand appear and beat up the opponent. The group now includes Keldeo).
Volt Crash, Ash and Pikacu's self made electric Hyper-Beam variant impresses Raikou enough that when he fights Ash he plans to throw the match just to learn how to do it.
The fourth movie, Celebi, Voice of the Forest, starts with Ash, after a long race and a six-on-one Pokémon battle, finally succeeding in capturing Suicune.
Team Rocket's attack on Vicious, the Iron-Masked Marauder. Vicious is more formidable than in the original timeline, thanks to a failed attempt at stopping him executed by some Team Rocket Grunts ending up giving him more Pokemon... So Jessie, James and Meowth showed up with all their considerable firepower and the Pokemon world equivalent of a V-22Osprey, starting a truly formidable battle.
Ash bringing Pikachu back to normal after he got transformed into a Shadow Pokemon.
At the movie's climax, Ash not only engages Vicious with his bare hands, he does an Implacable Man-style Slow Walk towards him, smashing Dark Balls out of the air as he tries to capture his Pokémon again.
After everything is said and done, two Celebi appear and explain that all the trippy time nonsense that just happened was because the gang broke time. That's not an easy thing to do.
They also created the Fairy type.
Amongst the time displacements that occur when time breaks, there is a scene of someone performing a Heroic Sacrifice to save the floating town of Pacifidlog from a tidal wave. That someone is Ash's father, in an incident mentioned all the way back in Ash's first conversation with Ho-Oh.
Hitmontop vs. Primeape. Hitmontop is practically unassailable when spinning on his head, and kicks hard. Then Primeape starts running at the same speed of the spinning, and then some, and manages to grab Hitmontop's tail. They get both thrown into a wall. Primeape lands worse... And it activates his Anger Point, bringing his already powerful Attack at its maximum, and then uses Thrash.
"By the way, I think he's knocked out."
Hitmonchan vs. Keldeo. Hitmonchan holds his own, at least before Keldeo learns to use Secret Sword as a ranged attack...
Perhaps not in the "Explosions and Battle" sense, but Todd recently got the latest issue of a Photography magazine... and thanks to his photographs of the mating dance of the Articuno, pretty much the whole issue is about him. Bit of heartwarming in there, but it's cool to see characters we love so much get the recognition they deserve for doing awesome stuff.
Misty vs. Entei. It started with Psyduck nullifying Entei's trump card (Sunny Day, that empowers Fire-type moves, weakens Water-type ones, and allows to fire Solar Beam without charging. Psyduck's ability is to prevent weather change), and it became only more awesome from that. In the end, Entei won... And was so tired he fell asleep immediately after finally defeating the newly-evolved Kabutops;
Ash vs. Raikou. Raikou was throwing the fight... And some of the things he did included shattering an Aura-made Bone Rush staff. Wonder what he would have done had he been fighting seriously...
Orville, the High Flying Pidgey, actually manages to fly higher up than Pidgeot. How high was he? Well, we don't find out, but Pidgeot was in the Stratosphere when she had to stop because her wings were icing up. And Pidgey just kept on going.
During the Whirl Cup, Misty manages to beat Ash. Who was using Suicune. Granted, he was only using Suicune and Misty had to use both Politoed and Kabutops, but it's still an impressive feat given that she lost to both of Suicune's brothers. Brock figures that this was because Misty knew exactly what Suicune was having trouble with beforehand from Ash's training, surprised Ash with Politoed's Water Absorb, and managed to use Ash's on-the-fly planning to her advantage by using Suicune's ice attacks to stymie her own agility.
The Elite Four were watching the match. Even them, the strongest trainers in Kanto and Johto found it awesome, to the point they had trouble commenting on it.
Pidgeot laying down the law to the three Legendary Birds as their temporary babysitter, while Lugia is traveling with Ash for a time.
Right. None of you is in charge. I am. And that's for two reasons. First, Lugia specifically recruited me to keep you three in line. Secondly, and more importantly, I know Aeroblast and I have a sustained speed in level flight three times greater than what any of you can achieve. I can reach out and touch you from miles off, and you can't stop me. Any questions?
And using it on Zapdos when he does try.
In chapter 83, the gang and Ritchie have to deal with Cipher in addition to dr. Namba's group of Team Rocket. Cipher, of course, is using Shadow Pokemon, much stronger than normal Pokemon... And stillgets trounced. In one case while having a Type advantage (a Shadow Tropius vs. Misty's Gyarados. One Ice Beam and Tropius was out). Then we have Lucario using the Hiryu Shotenha... And Ash punching out Nascour.
The gym battle against Jasmine in chapters 85 and 86:
Jasmine being Crazy-Prepared enough to: make her gym out of face-hardened rolled steel plates (that is, battleship armour) for trainers of high-powered Pokemon (like Ash); having platforms for the trainers in case someone floods the field (as Kingler does); having powerful fans to pump out poison gas (this in spite of Jasmine using Steel-type Pokemon, immune to Poison-type moves. Then again, a surprisingly high number of challengers uses Poison-type moves against her...) and drain the water when the field is flooded (turns out useful when having Magnezone around in the flooded gym turns out being too dangerous), among other things;
Ivysaur vs. Aggron. Aggron wins by surviving Fissure and then hitting Ivysaur with a last Heavy Slam;
Charizard vs. Steelix starts out in style, what with Charizard dealing with the Sandstorm by flapping down the sand and then fusing it... And it ends with Steelix knocked out and a wall (made of battleship armour) ''deformed when Charizard threw his victim into it;
Charizard vs. Empoleon. An Empoleon that flies by way of Aqua Jet. Charizard wins... But between the two of them, they destroy this gym too (or at least a wall of it). One made of battleship armour.
In chapter 86, Mewtwo reveals he can talk with his psychic powers. Not telepathically, but by producing sound with psychic energy.
In chapter 87, Ash catches Entei. It was just as awesome as the previous battles... And, for the first time, Hounhour's Beat up was neutralized (everyone else got at the wrong end of a gang-up from multiple shadow clones).
During the Pokemon Extreme race, Entei decides to race against Ash. Ash is being pulled by Donphan. Entei, to give himself an handicap, decides to pull a railway push cart with Suicune and Meganium on it... And still outruns Donphan (the only reason he doesn't win outright is that he had not registered). Oh, and he has started running late, so he had to catch up too...;
Casey takes part to the race with her Pidgeotto... And, thanks to her Pokemon evolving, it takes the photo finish to verify who won. She came up second, but had her Pidgeotto evolved one second earlier she would have won.
In chapter 89, Brock's Pokemon solving the situation when the ghostly Ninetales kidnapped Brock again.
Chapter 90 + 91 - Lake of Rage incident:
The first Mega vs. Mega fight in the whole story is Rocket Executive Tyson's Mega Tyranitar vs. Ash's Mega Heracross.
Also, during the last round of Misty vs. Red Gyarados, Lance shows up as in canon. But not to capture the Red Gyarados - he's here to test Misty's mettle by giving her a Keystone and telling her that there's Gyaradosite somewhere in the lake. Once Misty's own Gyarados does find it, this story gets a Shiny vs. Mega battle anime fans can only dream about.
And to cap it all off, once Misty does beat the Red Gyarados, Lance offers to let her keep the Keystone if she trades the Red Gyarados for it.
Not related to the Lake of Rage incident... But Rayquaza mentions that Arceus survived being hit by the dinosaur-killer meteorite.
Chapters 92 - 94: Mahogany Gym match vs. Pryce:
The day before the match, Ash finds out (but knows already) that Pryce's prickliness is due to his starter Piloswine leaving and not coming back when he was hurt. Ash tells the local Nurse Joy that he'll go find Piloswine... and does.
Nurse Joy: "Did he-"
Pryce: "Yes. He did."
Pryce's Glalie vs. Ash's Lucario should be a Curb-Stomp Battle in Lucario's favor, right? Well... That Glalie is a master at creating snow shields and keep the distance, and can create a dragon made of ice and make it fight. Took Lucario the friggin' Hiryu Shotenha to finally close range and punch the ice ball out...
Ash's Poké-evolution aura comes back to bite him again, when Pryce's Piloswine evolves and takes out Snorlax.
Aurorus showing Entei exactly how you overpower Kyurem's Ice-type attacks (not that it helps her win in the end). Oh, and that's not even the worst a Pokemon with Refrigerate can do...
Quilava vs. Mamoswine. All of it.
Todd gets another Legendary Bird photo op - with Team Rocket's newly acquired Moltres.
In chapter 92, Raikou challenges Chuck in a gym match... And his Chesnaught No Sells his Electroball before hurting him by blocking. Granted, she has the Ability Bulletproof (that makes her immune to ball and bomb moves), and the move Spiky Shield has that interesting effect, but still...
Also for Chuck for preparing that Chesnaught specifically for Raikou.