Parentheses indicates statistics in Japanese version.
Numbers and words in gray indicate coding unavailable in normal gameplay.
Sometime before, Bowser was launched out of a cannon on Stardust Fields and lost his memory after crashing. Popple soon found Bowser and decided to take him under his wing, dubbing him Rookie. Rookie then follows Popple around helping the bean thief in any way possible. Soon, at the Chateau de Chucklehuck, Rookie and Popple run into Mario and Luigi. The Mario Bros. recognize Rookie as Bowser, but Rookie only knows that the two look familiar to him. Popple then orders Rookie to fight with him against Mario and Luigi. After being defeated, Rookie and Popple run off into Chucklehuck Woods.
After exploring around, Popple and Rookie run into a dead end with the guardian of Chucklehuck Woods, Chuckleroot, blocking the way. Popple and Rookie decide to wait out nearby until someone (presumably the Mario Bros.), came along to open the path. Sure enough, after Mario and Luigi get past Chuckleroot, Rookie and Popple race off ahead to get the treasure. Unfortunately for them, they are captured by Bubbles who has them tied up over a barrel of Chuckcola. Then the barrel becomes alive, turning into a monster that sends Rookie and Popple away out of Chucklehuck Woods with a rapid spin.
Rookie and Popple are seen again in the basement of Woohoo Hooniversity trying to steal the Beanstar. However, Mario and Luigi arrive on the scene and all of them decide to fight for it. Rookie and Popple lose yet again but, before anyone can move, a Peachbot falls into the basement and laughs, causing the Beanstar to go mad again. Rookie, Popple, Mario, and Luigi all grab onto the Beanstar and fly out of the Hooniversity into the sky. Bowser regains his memory shortly, but then falls from the Beanstar and lands unconscious in Stardust Fields. His body is then used for a new evil.
In the 3DS remake, it's revealed that Captain Goomba fell on Bowser's head in Hoohoo Mountain and caused his amnesia. Afterward, Popple accidentally fed a starving Bowser, who followed him out of gratitude, leading to him becoming Rookie.
If Rookie is defeated first in any of the two fights, Popple himself will run away.
Go, Goomba, Go! • This Beans War • For the Love of Hammers • Winged Traitors • The Hoohoo Melee Brigade • The Great Hammer Barrage • Don't Fear Flying Foes • Goombas vs. Goombas • The Amnesiac Koopa King • Goombas Galore
Turnip Tantrum • Minions vs. Minions • Hunger Pains • A War of Shy Guys and Flybys • Battle Tail • Beanbean Crossfire • The Rival Trio • Larry's Fortress • Captain Shy Guy Trial • Professor E. Gadd's Research • Oh, Hi, Shy Guy! • Shell Brigade, Move Out!
The Sweet Smell of Soda • Deep Trouble • Forest Masquerade • Reclaim the Red Goblet! • Gold Beanie Appears • Invisible Leaderership • Ice Guys Finish Last • The Tough-As-Nails Squad • Forest Fight • Popple's Partner • Captain Goomba Trial (Gold) • Shy Guy Goes Overboard • King of the Boos
A Dry Bone to Pick • The Trouble with Toads • Flying Beans in the Desert • Find the Invincibility Mushroom! • Gold Beanie Spotted! • Silly Ol' Goomp • Ice Bros. Feel the Heat • The Lonely Koopa Troopa • Toad Rescue • Captain Koopa Troopa Trial • Popple's Partner, Part 2 • A Goomba Tail • A Muster of Masks
Goombas Unite • Gather the Cruiser Parts! • Power Play • Spear Party on Ice • Monochrome Explosion • Gold Beanie Fights Back! • Return of the Koopa Cruiser • The Trio's Last Stand • Captain Boo Trial (Gold) • Boo Party! • Shy Guy Barrage
Fireball and Boomerang Crossfire • Chain Chomp and Spike Stomp • A Tale of Tails • Double Trouble Koopaling Caper • Pokey Panic • Rumble in the Castle! • Gold Beanie's Final Stand • Goomba's Worth • Showdown Time!! • Believe in Bowser • Captain Boo Trial • The Mightiest Minions • The Beastly Bean Battalion
• ⋆-Enemy, boss, or stat exclusive to the main game. • ⋆⋆-Enemy, boss, or stat exclusive to Minion Quest: The Search for Bowser. • ⋆⋆⋆-Enemy variants differ in Mario & Luigi: Superstar Saga + Bowser's Minions.