Similar to "Recruit Gardevoir" in PMD B/R RT, we could have a category called "Defeat Darkrai" in this game.

After defeating Dialga, you are sent back to the guild to continue work. You are sent off to Sky Peak later on.

At some point around here you graduate from the guild and learn you are unable to evolve because of the disruption in space.

After exploring Sky Peak with Shaymin, Scizor goes missing. You rescue him from Froslass in Blizzard Island / Crevice Caves.

Next up is the Manaphy bit. You rescue an egg from a place Sunflora talks about, it hatches, you take care of the Manaphy (have Blue gummis ready!) and fight off Gyarados.

Then you explore Aegis Cave with some peppy exploration team, and have to get lucky with Unown drops/encounters to continue. Regigigas fight at the end of this dungeon.

Azurill is in a nightmare, and you have to go to Mt. Travail to bring Drowzee back.

Drowzee sends you into Azurill's nightmare. In the nightmare, you learn more about Palkia from "Cresselia". You are told to go to Spacial Rift.

Clueless as to how to get here (and Lapras doesn't even know) you and your partner don't do anything. That night, Palkia kidnaps you and brings you to Spacial Rift. You go through the dungeon and fight Palkia at the end, demanding answers.

Darkrai reveals himself as the Cresselia you've been talking to, and the entire story unfolds here. Darkrai demands you confront him at Dark Crater. You do so and defeat him. This is the true final boss of the game. You are given the option to save after the story comes to an end. Final time is checked here.

TA-DA! Consistency among categories across PMD series.

TAS of this category in under 7 hours.