The entrance of Shadow Lugia, one of THE MOST badass villain Pokémon in the franchise. 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. And she does! Instead of being useless or just a tutorial in the series, the player's mom is vital to the plot.
How do you top the typical Ceiling Peon routine? Do it on an elevator. Alternately, Kleef's clever approach of doing it after That One Boss.
A minor one when fighting Ardos. His shadow Snorlax knows the move Shadow End and its animation is to get up, jump in the air, and belly-flop the opponent. Let's repeat that: Snorlax belly-flop attack before Pulverizing Pancake was a thing. The enemy's not recovering from that.
Raiding the Shadow Pokemon factory with the help of Team Snagem, of all people. A large gauntlet of tough trainers with a challenging boss at the end and Cypher openly challenging you. Bring It.
The pan across Citadark Isle as an extended rearrangement of the title theme kicks in. It really hypes you up for the final stretch.