Later,An evil robotic scientist, sent a Thug Leader to hunt down Ratchet. While arriving at Florana,Ratchet,Clank,and Sasha notice those Boot Tracks. As they follow,They didn't notice a mysterious figure was watching them. By the time they got there,They were attack by a group of Monkeys. They have Ratchet challenge his opponent,who turned out to be Qwark. They are saved by a Figure,who introduced herself as Tawlyn Apogee. They head back to the ship with Qwark and his Monkey ally,Skrunch.
They learned that Qwark had lost his memories during the battle with Ratchet and Clank. Tawlyn explains that her father was the galaxy's leading expert on Lombax technology and thus may hold the secret to their disappearance. Tawlyn's Allie's,Cronkite and Zephyr uses the Projector to show Ratchet about during the Great War on the Lombax home world,Fastoon,the Guardian uses the Dimensionator so the survivors can escape. The Guardian manage to escape with his Son.
After watching the Vid-Comic of Qwark,He regained his memories. Qwark reveals that he knew about : He was on a Planet Magmos,confronting Nefarious. They fought each other until Nefarious knock off the Catwalk and fell into the Machinery of his base. As Qwark fled,He didn't of Nefarious' Tranformation.
Qwark decided to form the Q-Force,recruiting Big Al,Skidd,and Helga. Ratchet return to Veldin to talk to his adoptive Father,who explained that he found Ratchet on his doorstep as a Baby. The Q-Force are confronted by the Thug Leader and his goons. Suddenly,a Momma Tyhrranoid appeared and kill the goons. The Thug Leader fled while Ratchet and Clank defeated the monster.
Ratchet goes to Fastoon to find that the city is deserted. He found the Infobot which shows him that the Guardian saying I'm gonna be taking his Child so that he can survive. Ratchet realize that the Guardian is his father.
The Q-Force learned that the President is held captive by Nefarious. They battle with the Thug Leader,killing him in the process,but Skrunch is injured. Ratchet and Clank confronts Nefarious while he pilots his Warship along with Lawerence. Qwark damage it with his Fighter Jet,allowing Ratchet and Clank to destroy it. Nefarious survives and grab Qwark,but gets decapitated by Tawlyn.
Ratchet receives a hug from Tawlyn and Sasha. The President is free and congratulates the Q-Force,including Ratchet and Clank. Clank tells Ratchet that the Lombaxes could be out there somewhere. Ratchet assures him that wherever they are,They might be alive.
Mid-Credits:
Lawerence survives the destruction,but gets captured by Space Pirates while they were holding Nefarious' head. As they left it on the plate,Nefarious' eyes opens.