While playing chess in their penthouse in the Bogon Galaxy,Ratchet & Clank received word that the Veldin is under attack by an army of Tyhrranoids. They head there to fight off the invaders with the help of Sasha Phyronix,daughter of the President. They learned that the distress signal going on at Florana.
Later,An evil robotic scientist,Doctor Nefarious sent a Thug Leader to hunt them down. While arriving at Florana,Ratchet,Clank,& 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 attacked by a group of Monkeys. They have Ratchet challenge his opponent,who turned out to be Captain Qwark. They are saved by a figure,who introduced herself as Tawlyn Apogee. They head back to the ship with Qwark & his Monkey ally,Skrunch.
They learned that Qwark has lost his memories during the battle with Ratchet & Clank. Tawlyn explains that her father was the galaxy's leading expert on Lombax technology & thus may hold the secret to their disappearance. Tawlyn's allies,Cronkite & 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 Nefarious: He was on a Planet Magmos,confronting Nefarious. They fought eachother until Nefarious gets knocked off the catwalk and into the Machinery of his base. As Qwark fled,He didn't notice about Nefarious' decided to form the Q-Force,recruiting Big Al,Skidd,& 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 & his goons. The Thug Leader fled while Ratchet & Clank defeated the monster.
Ratchet goes to Fastoon to find that the city is deserted since the Great War. He found the Infobot which shows him that the Guardian saying "I'm gonna be getting my child to safety 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. Ratchet & Clank battle against the Thug Leader,killing him in the process,but Skrunch is injured. Ratchet & Clank confronts Nefarious while he pilots his Warship along with Lawerence. Qwark damage it with his fighter jet,allowing Ratchet & Clank to destroy it. Nefarious survives & grab Qwark,but gets decapitated by Tawlyn. The President is free and congratulates the Q-Force,including Ratchet & 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 and picks up Nefarious' head before being abducted by Strange beings.