- The whole main premise. All of Bowser's Minions are out looking for him after he vanishes, and band together to rescue him. And they're all being banded together by a single Goomba, who becomes the captain, driven by his loyalty to Bowser. What's more heartwarming is the fact that despite being shitted on and trashed on their entire lives as being useless and the lowest of underlings, one of their kind manages to rally the entire army back together and rescue Bowser, and manages to live up to the title that his small group only bestowed upon him because no one else wanted to do it, and earn the respect and admiration of the ENTIRE ARMY. He became his own character, and he deserved to be promoted at the end, even if he ended up losing his position in the end. Not to discount anyone else, but Captain Goomba, you are the MAN.
- The ending narration states that despite being stripped of his position, his former minions have never forgotten his leadership. This isn't the story of how he got his flag taken away, it's the story of how he turned into one of the best soldiers Bowser could ever afford to have, and the story of how he became a captain.
- Also the story's final image has a minor one. As Captain Goomba is fleeing from the incredibly furious Bowser, his 3 other captains, some minions and even the Koopalings, can be seen cheering him off as he runs away.
- After Captain Goomba is attacked by the amnesiac Bowser in Chucklehuck Woods, he falls down and cries for hours. When he gets up again, the other captains are still there, and cheer him up. It's a surprisingly adorable scene.
- The conversation at the end of Joke's End. Both parts of it. After Captain Goomba and the squad finally beat the Elite Trio for good and recruit them to their cause, for Private Goomp, who had spent the entire story as a rival jerkass going after Captain Goomba and constantly failing, to finally accept the much-deserving Goomba as their captain speaks all the messages. And for Captain Shy Guy, of all people, to express his admiration of the captain says a lot about how the kid has gone from being a random soldier in a Goomba squad to the captain of an entire army—and all of this, because after everything he and his troops have gone through, he will not give up on Bowser. No matter WHAT. It's honestly a wonder this guy isn't given any of the respect Mario and Luigi get--he accomplishes a feat only guys like ''them'' can pull off!Captain Koopa Troopa: Phew! What a ruckus.Captain Boo: Soon we'll be able to go home, back to Bowser's Castle...But first, we need to take out that Fawful jerk!(beat)Captain Boo: And you know, I must say...Goomba really came through and turned out to be a great captain.Captain Koopa Troopa: That's because his Goomba feet can take the heat! If a captain can't run, he'll have no fun! (He's a real...Yeah...I'm being ignored. I'm wasting my best material here.)Captain Boo: What?! You can't be serious!Captain Shy Guy: He reminds me of Lord Bowser.Captain Boo: Are you FEELING all right? Maybe you should lie down.
Captain Goomba: YES! We're back in business!(beat)Captain Goomba: Private Goomp...This place has me feeling all...nostalgic.(the scene flashes back to the beginning of the story, with the two Goombas, Captain Goomba and Private Goomp, in barrels after being defeated by the Mario Bros in the first tutorial battle)Captain Goomba (Goomba on the right): *sigh* I can't believe I got stomped AGAIN. Oh, well. I'll beat that stupid Mario next time...Let's band together next time. Strength in numbers and all.Private Goomp (Goomba on the left): HMM. That gives me an idea...Us Goombas should up our game! Get some respect for a change!(scene flashes back to the present, with Captain Goomba and Private Goomp in that same place)Captain Goomba: I'm with you, Private Goomp! It's time to make a name for ourselves!Private Goomp: Say what?(scene shows the Koopa Cruiser flying in the air)Captain Goomba: Let's show the world what Goombas are capable of! For Lord Bowser!Private Goomp: Oh, that. Sure.
- And later on, inside the Koopa Cruiser:
Heartwarming / Minion Quest: The Search for Bowser