One night Mario and Luigi watched stars falling from the sky, then they saw a strange star falling behind a Mushroom Hill which attracted their attention. As they quickly found out, it was not a star, but a spacecraft. The creature inside it told them there was a threat in their galaxy. If Mario doesn't stop it (with his army, apparently) the Mushroom Kingdom will also be doomed.
This game provides examples of:
- Chest Burster: The Continue screen shows a Piranha Plant exiting Mario's body in this manner◊.
- Disc-One Final Dungeon: The Shroob castle (or at least a place related to it) appears after a few levels. One would expect it to be the final dungeon as they're the alien invaders mentioned earlier, but it's only the halfway point.
- Face Hugger: The Continue screen shows a Blooper attached on Mario's face in this manner◊.
- Flying Saucer: Shroob UFOs appear as enemies.
- Game-Breaking Bug: Buying things from the shop is known to make the game freeze if you're playing on an emulator.
- Giant Space Flea from Nowhere: The Final Boss. The game's intro and levels greatly implied the threat would be Shroob-related, so why Fawful (in his Dark Star Core form no less!) out of all people appears at the end is anyone's guess.
- Playing with Fire: Mario can shoot fireballs after obtaining a Fire Flower, though they don't bounce off the ground like usual.