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This article contains plot details.
The game starts with Ratchet working on a hoverbike in Metropolis, Kerwan. Ratchet and Clank then receive a call from Captain Qwark. An army of robotic commandos, let by Emperor Percival Tachyon, have launched a full-scale assault on the city. Confronting the emperor, Ratchet is told that Tachyon is after him because he is the last Lombax in the galaxy.
Due to being outnumbered and overpowered, the duo flee. They decide they need to learn more about Tachyon and go to the Polaris galaxy in search of answers. During this, Clank is visited by the Zoni, small robots that only he can see. Clank is upgraded by the Zoni and they tell him that he is special. They also tell him that he must help Ratchet make a difficult choice during their adventure.
Along the way, the duo meet Talwyn Apogee, the daughter of Max Apogee, a famous explorer who disappeared. During their travels, they learn about the Great War that took place in Polaris long ago. In the war, the Lombaxes wiped out all of the Cragmites (Tachyon's species) and were considered heroes. How they managed it became known as the Lombax Secret.
Learning about Fastoon, the Lombaxes' deserted home planet, Ratchet and Clank travel there. On the planet, they learn that the Lombax Secret was a helmet called the Dimensionator. This helmet had the power to open wormholes to other dimensions. The helmet was used to banish the Cragmites but one was missed.
Tachyon was found as an egg and was raised by the Lombaxes. Tachyon came to despise them after learning about what they did to his species and that they took pity on him. He later launched an all-out attack on Fastoon. The Lombaxes sent themselves to an alternate dimension in order to escape but two were left behind, Kaden and his son, Ratchet. Right before Kaden was killed, he sent Ratchet to the Solana galaxy.
Ratchet and Clank attempt to get the helmet and keep it away from Tachyon. However, Qwark shows up and attempts to destroy it himself, wanting the spotlight. Qwark fails and this allows Tachyon to steal the device. Tachyon tries to tempt Ratchet into opening a wormhole to the Lombaxes' dimension but Clank convinces him not to.
Ratchet and Clank engage in a battle with Tachyon. During the fight, the Dimensionator is damaged and it opens a black hole that Tachyon falls into. The device then becomes irreparable.
During the celebration of Tachyon's defeat, the Zoni show up, this time appearing to everyone. The Zoni tell Clank that he must go "home". Despite Ratchet's protests, Clank "willingly" goes with them. The game ends with Ratchet too stunned and helpless to stop them.
The game received near universal praise.
- Spike TV Awards: Best PS3 Game (Won), Best Action Game
- Gaming Target: "52 Games We'll Still Be Playing From 2007" selection
The game also a runner-up for IGN's PS3 Game of the Year award in 2007.
- The game says that only two Lombaxes were left behind, Kaden and Ratchet. However, this is incorrect as Angela Cross, a character from Ratchet & Clank: Going Commando, and Alister Azimuth, a character from Ratchet & Clank Future: A Crack in Time, are also Lombaxes.