Koops first meets Mario in Petalburg. He doesn't say much, but before Mario leaves to another part of town, he stops the latter, however Koops' shyness overcomes him and he goes back. When Mario goes off to Hooktail Castle, Koops stops him again and cries that he wants to join Mario's party in order to avenge his 'dead' father, but not before Koopie Koo finds out. She begs him not to go, but he says that his goal is to be a strong Koopa for her, which makes Koops' girlfriend mad, and results her to withdrawing into her shell and firing herself at Mario and Koops.

Inside the castle, Koops finds a skeleton that he believes is his father's. Reading the note the corpse was grasping reveals it was actually Kolorado's father, and Koops blushes while being slightly embarrassed, but then wonders if any of the other skeletons is his father.

When Mario and Koops first meet up with Hooktail, the dragon remarks that they look similar to one that passed by here recently, then the battle then starts. Once the fight is finished, a near-dead Hooktail spits up Koopley, who was living in Hooktail's stomach for ten years. After a reunion with his son, Koopley reveals he found the Diamond Star in Hooktail's stomach, and allows Mario to take it.

After assisting Mario in his quest to collect the rest of the Crystal Stars and save Princess Peach, Koops returns to Petalburg where he makes plans to marry Koopie Koo and run for mayor.

Koops is the only partner with a defense of 1. However, he has the lowest health of all partners at Super Rank and regains this status at the Ultra Rank with Ms. Mowz (Koops has 15 and 25 Health Points, respectively). Furthermore, if an enemy jumps on Koops and the player isn't able to defend him by using an Action Command, this partner gets flipped over and cannot move while also losing a defense point, much like the other Koopa Troopa enemies as well.