Ratchet and Clank is a third-person platform shooter game. The playabe character is Ratchet, though Clank is playable in certain portions of the game. Ratchet fights his enemies with an array of weapons (Clank uses his fists) and he traverses various environments. Clank has different gameplay, though traversing planets and controls remain the same. Players progress through the game by moving from planet to planet. New planets are unlocked when objectives on previous planets are achieved. Weapons are also unlocked, though some can be bought from vendors.

Shiv Helix is being transported to a prison where his cellmate is someone of whom he has been a huge fan, Captain Qwark. Ratchet is in the process of rescuing Clank. Ratchet is on the planet Valdim where he is acting as a mechanic for his father Grim. Captain Qwark sees the duo Ratchet and Clank and informs them of an assignment. Recognizing that his next opponent is on Valdim, Captain Qwark negotiates with Deck whilst his troops fight the Rangers off the planet. All this Qwark does to spite Ratchet.

During the fighting Ratchet steps aboard the ship Phoenix and inflicts serious damage before Clank disables it. Ratchet enters the Deplanetizer with the intention of disabling it, but Deck immobilizes him. Deck secures Ratchet into an escape pod and blasts him into space whilst the Rangers watch the destruction of planet Novalis.

For several weeks, the loss of Qwark's leadership stiffles the Rangers whilst Deck destroys five planets. When Ratchet returns to Valdin, he decides to take the blame and quit. Clank tried to disuade him, as the Blarg were ready to destroy the final target:Planet Umbris, whose destruction will cause the destruction of other planets due to its orbital convergence. Ratchet deduces the truth: Nefarious, anguered by his defeat at the hands of the Rangers manipulates Drek, using his resources to destroy the planet whilst discrediting them. With his confidence restored, Ratchet returns to the planet Kalebo III, where the Blarg have attacked the headquarters of Gadgetron so as to gain access to their high tech weaponry. The company chairman asks them to rid the planet of attackers, with a Holo Guise being the prize. With the prize won, Ratchet confers with other Rangers and enters the Deplanetizer.

An increasingly disillusioned Qwark confronts Drek over his failure to keep his promise of not attacking the Rangers anymore. Nefarious mocks Qwark for his treason before sending him on his way. As Drek comments on how well their alliance is going, Nefarious turns him into a sheep and ejects him into a capsule that goes into the artificial planet. Meanwhile, Ratchet, disguised as Qwark, stops the use of the Deplanetizer's power core, thereby doing away with its firing capabilities. When the real Qwark shows up, he tries to kill them all until his jetpack fails. Realizing the errors of his ways, Qwark appoints Ratchet the head of the rangers so as to get Nefarious into custody. Instead, Nefarious dons a mech suit and manoeuvres the Deplanetizer to crash directly into Umbris. The duo lure Nefarious into the gravitational pulm l of the planet, thereby causing him and his suit to spontaneously combust.

With the Deplanetizer's destruction, Ratchet, Clank, and Qwark grab a teleporter and escape off of the planet before it destructs.

In the present, Qwark and Helix are collecting rubbish near the Hall of Heroes. Ratchet and Clank come out and greet Qwark. Seizing the opportunity, Helix steals Ratchet's ship and escapes. When the duo decided to pursue him, they offered Qwark to join them, which he did.

The game was announced at Sony's press conference at E3 2014. Developers from the first game, such as design chief Brian Allegeiec, were brought on for the subsequent game. The game was slated for 2015, but was released in 2016 to coincide with the film.