The story begins on a backwater planet in the Solana Galaxy known as Veldin. Here we see our protaganist Ratchet working on a space ship. We get our first glimpse of the Help Desk as he checks it to see what else needs to be done to complete his ship. A robotic ignition system is needed. Meanwhile at a robot manufacturing plant elsewhere in the galaxy we witness the glitch that brings us our next protaganist Clank a tiny robot who discovers that his creator Chairman Drek plans to create a new planet by destroying other planets in the galaxy. He is spotted as he flees the planet and is shot down over Veldin. Ratchet strikes a deal with Clank. If Clank will start his ship he agrees to help Clank locate Captain Qwark to save the galaxy from Drek. The two begin an adventure. They eventually find Qwark only to discover he is working for Drek. Ratchet vows to pay him back while Clank tries to convince him that Drek is the bigger issue. Ratchet after searching vigorously finds and kills Qwark. The two go on to save the galaxy from Drek by destroying him his planet buster and his newly constructed planet. The two become instant celebrities and are featured on many magazine covers and television show. They settle on Veldin to await their next adventure.

After defeating Drek in the previous game Ratchet and Clank become celebrities. However things start cooling down after a while. After an interview with Behind the Hero Ratchet and Clank are suddenly teleported to the Bogon Galaxy by Abercrombie Fizzwidget the founder and CEO of Megacorp a company that makes everything from household appliances to heavy weaponry. Fizzwidget asks the duo for their assistance in recovering a stolen biological experiment called the Protopet. Then Ratchet receives weeks of training to prepare him for the missions he will be assigned. (This training includes Martial Arts, Heavy Weaponry, Stealth, Camouflage, Survival, Ballroom Dancing, and Origami.)

Ratchet flies to a flying lab in Aranos, and searches for the Protopet. Eventually he finds the Protopet in a cage only big enough to fit the biological experiment on a pedestal. The thief reveals himself and Ratchet attempts to lie about his business on the ship. The thief takes the protopet and leaves the ship. Ratchet returns to his ship and contacts Fizzwidget saying that the thief escaped and he had no idea about the whereabouts of the thief.

Ratchet is given coordinates by Fizzwidget and chases the thief across several planets. Eventually Ratchet confronts the thief on the frozen planet Siberius. He defeats the thief, reclaims the experiment and returns it to Mr. Fizzwidget. Later after Mr. Fizzwidget accidentally ejects Ratchet and Clank from their ship the thief approaches demanding the experiment back, not realizing that Ratchet doesn't have it. The thief's mask comes off accidentally, and it's revealed that he is actually a girl Angela Cross. After learning that the experiment has been handed back to Megacorp, she warns that it will ultimately doom the galaxy.

On planet Dobbo, Ratchet and Clank discover that Angela's claims are true (the experiment turns out to be a dangerous predator) and try to persuade Fizzwidget to destroy the experiment, but their efforts are in vain. The duo then stumble across an ad for the Protopet (the experiment) which is being prepared for mass release. On planet Boldan, Ratchet and Clank are captured for attempting to bump off Mr. Fizzwidget (at this point and time, Ratchet was threatening a poor-quality robot Fizzwidget look-a-like.) They are sent to a prison, but escape and rescue Angela, who has also been captured by the Thugs. Eventually the three of them go to Megacorp HQ to end the Protopet menace once and for all.

After they get there the female Infobot (who then gets zapped by Qwark) reveals that Captain Qwark (the disgraced superhero from Ratchet & Clank) was planning the protopet invasion all along. Qwark was about to use the Prototopets to restore his reputation He takes Angela's Helix-o-morph (a gadget that will repair the fatal flaw in the Protopet) and zaps the original Protopet. But something goes wrong, and the original Protopet mutates into a gigantic monster. When Ratchet finally defeats the Protopet Clank discovers that the batteries in the Helix-o-morph are in backwards. Angela corrects this, and after she zaps the original amplifies the device with Megacorp's TV transponders to cure all the Protopets in the galaxy ending the threat once and for all. The real Fizzwidget then appears who was tied up in a closet the whole time. Ratchet picks up the smashed Infobot and repairs her. In the end of the game we see Ratchet Clank Angela (aka the Thief) and the Infobot back at Ratchet's home where they find out that Qwark is now paying back for his misdeeds at the Megacorp Testing Facility unwillingly being a test subject for Megacorp's new Crotchitizer - enough said!

Channel surfing past Clank's new TV show "Secret Agent Clank" Ratchet stumbles across a news report about his home planet Veldin being under attack by an army of aliens named Tyhrranoids. The lead suspect is a robot by the name of Dr. Nefarious. After racing to Veldin and being crowned as the new sergeant for the Galactic Rangers they are contacted by the President on the whereabouts of the only man who has ever defeated Nefarious. It turns out it was Captain Qwark who apparently lost his memory while working to save the Florana Jungle's fauna. He now believes himself to be a monkey. After Qwark and his companion Skrunch (a one-eyed monkey) are led to the ship, Sasha, captain of the Starship Phoenix has been ordered to assist Ratchet and Clank.

Aboard the starship, they leave Captain Qwark in his new quarters. After leaving Qwark they find Sasha listening to a transmission from the president on planet Marcadia, who turns out to be her father. After that Nefarious intervenes the transmission and declares war on the "Squishies" or organic life forms. Ratchet and Clank then venture out to Marcadia's capital to assist the Galactic rangers and the president. After assisting the president Ratchet and Clank return Qwark's memory by playing a video-comic (Vid-comic), and is sent to Annihilation Nation to claim the Tyhrraguise (a device which conceals the wearer as a Tyhrranoid) as prize. However, after claiming the Tyhrra-guise, Ratchet and Clank are informed that the president has laid the outcome of the war into Qwark's hands.

The "Q-Force" (Big Al, Helga, Skid McMarx, Ratchet, Clank, Qwark and Sasha) is assigned a new mission (rather Ratchet's new mission) to infiltrate Nefarious' base on Planet Aquatos to acquire as much information on Nefarious' plans as possible. They find that Dr. Nefarious is Clank's biggest fan along with an encrypted star-map to the Tyhrranoids' home planet and base, Tyhrranosis. Nefarious and his butler Lawrence are shocked to see that their base has been infiltrated, and later find out Qwark is behind it. After Al decrypts the starmap and the group (mainly Ratchet and Clank) infiltrate the base on Tyhrranosis and destroy it Dr. Nefarious sends the Q-Force a transmission still shocked that they actually infiltrated his base. Al traces the transmission to planet Daxx and before leaving Ratchet acquires a new gadget from Helga the Hypershot a combination of the Swingshot and the Dynamo.

When he lands, Ratchet is led by Al to a computer terminal that contains data on Nefarious' new secret weapon called the Bio-Bliterator. Clank also finds that a transport ship had just left for the Obani Gemini moons the day before. Ratchet, Clank and Skid make their way through the first two moons only to find the third is protected by a "Omega Class Disintegration Shield". Ratchet then gets an urgent call from the Galactic Rangers who need his help on Blackwater City against the Tyhrranoids. Ratchet leaves to help them, but Skid decides to stay and work on the force field. Ratchet and Clank arrive on planet Rilgar and help the Q-Force defend their base. The pair soon set out to find they need to find Courtney Gears, a pop-star singer they believe is working with Nefarious. Ratchet and Clank return to the set of Annihilation Nation to find Courtney Gears, begging to be in one of Clank's movies. When Clank asks for info on Nefarious she knocks him out and brings him to Nefarious herself. He gives Clank a choice - join him or die with the "Squishies". Back at Clank's trailer, Ratchet is ambushed by the Tyhrranoids. Fighting his way back to the ship he finds Clank who is acting very strange. Ratchet asks him about Courtney but all Clank says is that Nefarious' star cruiser is named the Leviathan.

The two land on Obani Draco the third moon where Skid was able to bring the shield down. As it turns out it is Courtney's hideout. The two discover the Bio-Bliterator there, a machine that changes organic life forms into brainwashed robots bent on destroying the "Squishies". After that they confront and defeat Courtney Gears. Upon finishing her off, they receive a transmission from Sasha who tracked the Leviathan to the Zeldrin Starport. Leaving Skid who has been transformed into a robot by the Bio-Bliterator because he was a test subject. They head for the starport to meet up with Qwark.

The Q-Force reach the Leviathan and fight their way through hordes of enemies until they find Nefarious waiting. It turns out that it was a trap as he activates the self-destruct system and warps out of there. All of the Q-Force returns to the Phoenix except for Qwark who stays behind, saying he thought he saw something. Ratchet and Clank fly off just as the Leviathan explodes still debating whether to leave Qwark behind.

After a funeral for Qwark on the Phoenix Ratchet flies to the city of Metropolis which is under attack by Tyhrranoids. During the battle Nefarious uses the Bio-Bliterator to turn hapless citizens and Tyhrranoid invaders alike into robots. Ratchet battles his way to a hovering train where it is revealed that the real Clank has been the prisoner of Doctor Nefarious ever since an evil copy known as Klunk replaced Clank and met with Ratchet at Holostar Studios. After defeating Klunk Ratchet and Clank are reunited and they fly to the planet Zeldrin to investigate the wreckage of the Leviathan hoping to find what Qwark was looking for.

On Zeldrin, they discover an encrypted data disc (The Master Plan) and a recording that reveals that Qwark was alive when the cruiser went down. They resolve not to tell the crew that Qwark is alive until they find out why he didn't report to the Phoenix. After playing a video game that contains information as to the whereabouts of the Quark's hideout they fly to the Thrann Asteroid Belt and battle past security robots and hostile Lawn Ninjas (invented by Megacorp) until they find Captain Qwark himself, who has abandoned his fight against Nefarious in favor of the comfort and safety of his hideout. Ratchet leaves in disgust but Clank makes one last appeal to Qwark stating that he had an opportunity to "become the hero you have always wanted to be".

When they return to their ship, they receive a garbled transmission from Sasha, who tells them that the Phoenix is under attack. Ratchet helps the Galactic Rangers regain control of the ship and free the captured Q-Force members. Al tells Ratchet that he has finally cracked the encryption on the data disc, which contains a complete copy of Nefarious' battle plans. Ratchet must fly to the planet Koros to destroy the Bio-Bliterator before it is unleashed on his beloved home Veldin.

Ratchet and Clank reach Koros and after battling hordes of Nefarious' troops Clank uses the ion cannon there to destroy the Bio-Bliterator. However Sasha soon reports that a second Bio-Bliterator is housed at a command center on planet Mylon guarded by an entire army of robot Tyhrranoids. Ratchet and Clank fly to Mylon, fight through the command center and reach the Bio-Bliterator just in time for Dr. Nefarious and Lawrence to escape. Luckily a dropship arrives for Ratchet and Clank to pursue Nefarious to his launch site.

At the launch site, Ratchet and Clank battle Dr. Nefarious once and for all. After a short while he falls down and begs for mercy fooling Ratchet into a false sense of victory before running away. Ratchet chases after Nefarious and with the help of the Galactic Rangers, defeats him. Nefarious and Lawrence then warp into the Bio-Bliterator which transforms into a giant robot. Ratchet and Clank look utterly doomed- when Captain Qwark flies in to fight alongside them. Ratchet and Captain Qwark engage in aerial combat against Nefarious and the Bio-Bliterator and destroy it. The Bio-Bliterator self-destructs and Nefarious and Lawrence are warped away to an unknown location.

Cut to the premiere of the latest Secret Agent Clank episode where Clank and Skrunch face off against Maximillian's forces on a snowy world. The premiere is a huge success, and Ratchet even gets a kiss on the cheek from Sasha.

The last scene is of Dr. Nefarious and Lawrence sitting on an isolated asteroid out of range to teleport to escape for the next several thousand years. Lawrence suggests some music to help pass the time but Nefarious only screamed out Lawrences name in anger.