When Conker first discovers Rodent, he is tied up in a Tediz base an about to be executed by a firing squad. After defeating Rodent's captors and freeing Rodent, the soldier squirrel decides to aid Conker in sabotaging the Tediz base.
Due to the fact that Rodent wears a prototype, indestructible armor, he actually allows Conker to use him as a shield as the two squirrels navigate they're way through the Tediz base.
After clearing they're way through the bulk of the Tediz base, Conker and Rodent happen to come upon a little girl. Against Rodent's protests, Conker decides to rescue the girl, with a reward in mind.
Eventually the girl reveals her true nature, she is apart of an abomination simply dubbed "the Experiment". Conker and Rodent are forced to due battle against the giant monster in a tank.
After the Experiment's body is destroyed, the little girl portion of the creature sends several Spider Mines at Conker's tank; the mechanical bombs end-up blowing up the tank with Rodent still in it.
Conker, thinking Rodent to be dead, quickly flees the scene as the little girl had activated the self-destruct mechanism in the Tediz base. Seconds before the base explodes, Rodent manages to dig himself out of the rubble of the tank; before Rodent can act, the base explodes.
Rodent survives the explosion of the base thanks to his armor. Instead of being blown to smithereens, Rodent was sent sailing through the air and ended-up crashing into the windmill in Windy.
When Conker and Rodent next meet it is in the rubble of the aforementioned windmill, Rodent having destroyed it when he landed. After a brief conversation the two squirrels part ways, with Conker refering to Rodent as an "idiot" and "retard" under his breathe, though it could've been done because Conker was frustrated at the time.
Rodent was last seen in "King Conker's" recently acquired castle in the closing cinema of Conker's Bad Fur Day/Conker: Live & Reloaded.