His very introduction being the CMoA where he quits Team Snagem, takes their Pokémon Snag system, and then blows up the base itself as he escapes, all while grinning like a maniac. Nothing is more badass than that.
Except for right after that, when he reveals himself to have 2 different evolutions of a Pokémon that there's just one of in most games. Not only does Eevee evolve into Espeon & Umbreon through Friendship, they start out at Level 26, when most Trainers start out with one Pokémon at Level 5.
Ho-Oh shooting down Evice's copter with Sacred Fire.
Eagun defeating some Cipher goons with his Pikachu.
The entrance of Shadow Lugia, THE MOST badass villain Pokémon ever! I mean, how many other Pokémon do you know have the strength to lift a freaking ship out of the water?
Even though they're the villain organization, you still have to give Cipher credit for replacing all the residents of Phenac City.
The ONBS raid shows why Cipher is a force to be reckoned with. In addition to the Elevator Peon and regular Ceiling Peon deployment, Exol's squad puts everyone under lock and key, they KO the bouncer, Megg is taken hostage, and Secc doesn't want to cause a panic by reporting all of this. Why go to all the trouble? Michael got a Data Disc from Lovrina after chasing her off, and they want to keep the data from being compromised with as little public backlash as possible. They do this by scrubbing the ONBS database!Ghetsis, put that in your pipe and smoke it.
So Prof. Krane's been kidnapped, workers are injured, notes for the Purification Chamber taken, all hope seems to be lost... but Lily decides to screw all that. So what if things went horribly wrong; she intends to rally the group and finish the job together.
A minor one when fighting Ardos. His shadow Snorlax knows the move Shadow End and it's animation is to get up, jump in the air, and belly flop the opponent. I repeat: Snorlax belly-flop attack. The enemy's not recovering from that.