Spoilers are unmarked per policy.
- The partner's development as a whole. Starting off too scared to even walk onto the guild's front door. Slowly develops more and more until they become badass enough to (with the main protagonist) defeat multiple Legendary Pokémon (which are minor GODS in the Mystery Dungeon universe) without even evolving. If the game was any longer, they'd probably fight Arceus himself and win.
- Wigglytuff showing Team Skull exactly why he has his reputation.
- Made even better after Generation VI-Wigglytuff is now part Fairy-type, and should be weak to every single member of Team Skull!
- Chatot's Heroic Sacrifice in Brine Cave (he survives). It was a Rescued from the Scrappy Heap moment for many.
- Grovyle's Heroic Sacrifice after the battle against Dusknoir (he also survives).
- Defeating Primal Dialga as two unevolved Pokémon.
- The so-called graduation test after the main storyline. Taking on "The Grand Master of All Things Bad"note is one thing, but doing so with only your partner as your sole ally? You're definitely showing your mettle by defeating them, and proving to the game that you're ready for the harder post-credits dungeons, since it takes preparation and strategy to take ALL of them down in one big boss battle.
- Drowzee sending the heroes into Azurill's nightmare was cool. What's even cooler? Saving them from the Big Bad Darkrai himself. Ridiculously awesome when you realize that his moment of suddenly showing up saved the heroes and scared Darkrai away.
- On top of that, he (along with a few others) were perfectly willing to go with you to Dark Crater to defeat Darkrai. It wasn't to be, but the fact remains that many Pokémon were ready to help out. Also a Heartwarming Moment.
- The player breaking free out of Darkrai's nightmare by attacking him, realizing their partner would NEVER give up no matter what.
- Palkia intervening when Darkrai tries to escape, resulting in Darkrai getting amnesia.
- In Special Episode 1, "Bidoof's Wish", Bidoof is alone, beaten up by Snover and his rogues Bagon and Gligar, and about to be robbed, when suddenly the entire Guild appears and thoroughly curbstomps the robbers in an epic battle for daring to hurt him.
- Special Episode 3, "Today's 'Oh My Gosh'", is rather underrated, for the moment when Sunflora apprehends the "invincible" Haunter:Sunflora: There's no such thing as an invincible Pokemon! It was nothing but a ruse, right from the beginning! It wasn't invincibility or anything else! Was it, guys?!Haunter: G-guys...What do you mean?! You found this out?!Sunflora: Yes. I figured out there isn't just one of you. Come on out! The rest of you! (uses Razor Leaf to bring out the other two Haunter)
- Wigglytuff being the only one to figure out Ditto's ruse in "Here Comes Team Charm".
- Special Episode 5, "In the Future of Darkness", allows you to play as Grovyle. And in the end, you team up with Celebi and a reformed(?) Dusknoir in order to fight Primal Dialga.
- While ineffectual, the Sableye unhesitatingly attacking Dialga when Dusknoir is threatened.
- You can make up to Chatot by having a perfect Sentry Duty score after the Perfect Apple Incident.
- The first time you use a strong hit-all move on a Monster House.