The stage begins with Fox and Diddy Kong, battling through their way through the swamp. After making it through part of the swamp, Diddy and Fox are walking and talking, but unexpectedly, a black, ethereal arrow is shot through Diddy, turning him into a trophy. Fox turns and sees Bowser holding a Dark Cannon, which he shoots again at Fox, but Fox dodges and slides, while Bowser points to Diddy's trophy, just as Shadowbugs devour it. Fox looks at this in a surprised state, and then turns and looks at Bowser, who is ready to make another shot at Fox. Blasts are shot around Bowser, who seems to almost trip.
An Arwing flies overhead, and Falco ejects himself from it. He lands, and dashes up to Bowser (possibly using Falco Phantasm, as the sound effect for it can be heard) and kicks the gun upwards and does a flip. He lands and starts shooting the Cannon with his Blasters, and the Cannon is destroyed. Bowser jumps backwards, and lands in his Koopa Clown Car, and flies away. After this, the Shadow Bugs turn the trophy into False Diddy, which then grows much larger. Fox revives Diddy's trophy, and a boss battle starts against False Giant Diddy. After winning, Diddy will cheer, while Falco walks away. Diddy drags him back and tries to tell him what is happening, but Falco once again walks away. Diddy grabs him and drags him away in the same manner that Diddy did with Fox; and while Falco is dragged away, Fox shrugs.
The three continue through the swamp, battling many enemies (most of them being Bowser's underlings). After making it through the swamp, Diddy, Fox, and Falco (standing at the top of a waterfall) spot a platform with Primids on it (ascending to the Isle of the Ancients), and Donkey Kong's trophy. Diddy stomps the ground, mad, but Falco glares over towards the other side of the waterfall, and the Great Fox appears. Falco then joins the player's team.
After clearing the Emissary, the player can return to this stage, enter a newly placed red door, and be taken to Pokémon Stadium 2. There, the player will fight Jigglypuff. If defeated, it will then become unlocked as a playable character and join the party.
- On the first part, Bramble Blast plays.
- During Falco's entrance, Area 6 plays briefly.
- While fighting Giant False Diddy Kong, Airship Theme (Super Mario Bros. 3) plays.
- Afterwards, the music switches to Yoshi's Island.
- During Jigglypuff's cutscene and battle, Pokémon Center plays.