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.