* Defeating [[spoiler:Primal Dialga]] as two unevolved Basic Pokémon.
* One of the special episodes available in ''Explorers of Sky'' allows you to play as Grovyle. And in the end, you team up with a [[spoiler: reformed Dusknoir]] and Celebi in order to fight Primal Dialga, with epic music playing in the background.
* Another special episode, "Bidoof's Wish", has the moment when 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 curb-stomps the robbers in an epic battle for daring to hurt him.
** Even better if you somehow manage to take them all on and win. TheBattleDidntCount is in full effect, but still.
* There was Chatot's [[spoiler: HeroicSacrifice]] in Brine Cave. It was a RescuedFromTheScrappyHeap moment for some.
* [[spoiler: TheAtoner Drowzee]] sending the heroes into Azurill's nightmare was cool. What's even cooler? Saving them from [[spoiler: The BigBad ''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 [[spoiler: Dark Crater]] to defeat [[spoiler: Darkrai]]. It wasn't to be, but the fact remains that many people were ready to help out. Also a HeartwarmingMoment.
* The special episode "Today's 'Oh My Gosh'" is rather underrated, for the moment when Sunflora apprehends the "invincible" Haunter:
-->'''Sunflora''': I have... I have proof that you're not invincible!
-->'''Sunflora''': There's no such thing as an invincible Pokemon! It was nothing but a ruse, right from the beginning! [[WHAMLine 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)''
** Loudred then helps her beat the trio and arrest them as deserved.
* [[spoiler:TheHero breaking free out of Darkrai's nightmare by ''attacking him'', realizing their partner would NEVER give up no matter what.]]
* The first time you use a strong hit-all move on a Monster House. Linked Charge+Discharge is recommended.
* Wigglytuff showing Team Skull exactly why he has his reputation.
** Made even better now that Gen. VI is out-—Wigglytuff is now part Fairy-type, and should be weak to every single member of Team Skull!
* Wigglytuff [[spoiler:being the only one to figure out Ditto's ruse]] in "Here Comes Team Charm".
* [[spoiler:Palkia intervening when Darkrai tries to escape, resulting in Darkrai getting amnesia.]]
* Grovyle's [[spoiler:HeroicSacrifice after the battle against Dusknoir]].
* While ineffectual, the Sableye [[spoiler:unhesitatingly ''attacking Dialga'' when Dusknoir is threatened]] in "In the Future of Darkness".
* 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 s/he becomes badass enough to (with the main protagonist) [[spoiler: defeat two (and more) "Legendaries" (By 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. the hero was arguably [[spoiler: already a Badass before the events of the game and it just came naturally, as the hero and the partner are kind of the Mario and Luigi of the team]]
* The so-called graduation test after the main storyline. Taking on [[spoiler:your Guildmaster and the rest of your guildmates--sans Bidoof]] 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 dungeons in the epilogue, since it takes preparation and strategy to take ALL of them down in one big boss battle.