When Ratchet and Clank are double-crossed by Luna, who was originally believed to be a kidnapped damsel, the duo is separated.

As such, he makes his next appearance afterwards, with a reduced role. It is presumed that Skrunch had stuck with Qwark during the events of Deadlocked, who were not kidnapped and forced to participate in DreadZone as Ratchet, Clank and Al were. During the applausal, seeing Ratchet get kissed by Sasha, Skrunch attempts to imitate by pouting at Clank, who immediately rejects a kiss from him. As Clank shoots a banana at Maxmillion, leading Skrunch to attack his helicopter and defeating him. Qwark has seemingly given up in the mission, and Skrunch expresses his disapproval over that decision.ДЄfter the defeat of Nefarious, Skrunch appears on the premiere of the upcoming Secret Agent Clank holofilm. When they reach Qwark himself, Skrunch assists Clank in deactivating the forcefield leading to his bedroom. He also watches Ratchet play the final Qwark vid-comic that hinted the location of his hideout, and requests to accompany the duo to search for him. Believed to be dead, a funeral is held for Qwark, which Skrunch attends.ДЄs Ratchet and Clank investigate the crash site where the starcruiser landed, Skrunch follows them, and together they find a hint that Qwark did in fact not die. Skrunch sticks with Ratchet as they try to wait for Qwark to arrive, but he doesn't. When revealed to be a trap, Nefarious activates a timed countdown to blow it up, and Qwark splits from the others to retrieve a datadisk. Here, Skrunch confronts Qwark over their past in the jungle, and once Ratchet arrives, they proceed to infiltrate Nefarious's starcruiser. Skrunch is next seen at the Zeldrin Starport, who is with Qwark as they wait for Ratchet to arrive. The rewritten script revolved around the two putting their differences aside to make their way through a chase sequence, with Skrunch once again crossing obstacles for Clank using the BGAMD. When Ratchet is fired from the Secret Agent Clank holofilm set, the role is reassigned to Skrunch. He continues to assist the Q-Force, as he joins Ratchet and Clank during their base on the Korgon Base, controlling the turret on a turboslider vehicle.

He joins Clank as he splits from Ratchet, and Clank uses a Banana Guided Autonomous Monkey Device (BGAMD) to direct Skrunch across obstacles, and allowing Clank to cross them. He mainly spends his time in the cockpit of the Starship Phoenix, but assists in the plan to infiltrate Nefarious's base on Aquatos. Following the formation of the Q-Force, Skrunch is assigned as a member. Ratchet and Clank fight and defeat Qwark in battle, who extract Qwark from the planet, and Skrunch follows them. As Qwark confronts them, Skrunch then hops onto Qwark's back, who forces the duo to run the path of death.

As Ratchet and Clank arrive and run into Qwark unknowingly, Skrunch is first seen hanging on Clank, who is on Ratchet's back. Over time, he would lose his memory and distanced from his personality, believing he was a Florana tree beast. Some time after the events of Going Commando, Captain Qwark moved to Florana for some time, befriending Skrunch.

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