The duo successfully foil an attempt by the invaders to destroy the Hall of Heroes by ramming it with a train loaded with explosives. Traveling to Kerwan, they discover that Drek and his Blarg soldiers have already invaded the planet. Ratchet names him "Clank" and offers to take him to the Ranger Headquarters on planet Kerwan. After the ship crashes on Veldin, Ratchet rescues the defective bot, who explains that he needs to warn the Galactic Rangers of Drek's plans. However, a defective warbot manages to escape using a stolen ship. Nefarious, an evil scientist who was presumed dead after his defeat at the hands of the Rangers. Meanwhile, in a factory on planet Quartu, Chairman Alonzo Drek of the Blarg oversees the construction of a mechanical army with his ally Dr. Despite passing all of their tests with flying colors, the Rangers refuse to accept him after learning of his criminal past. On planet Veldin, Ratchet, a young Lombax who works as a mechanic, dreams of joining the Rangers. Eager for attention, Qwark agrees to tell Shiv his side of the story. As Shiv happens to be a huge fan of Qwark, he reveals that a "hologame" is being made based on his last adventure. Prisoner Shiv Helix is being moved to a joint cell with the newly imprisoned Captain Qwark, former commander of the legendary Galactic Rangers. After completing the game, the player may choose to enter " challenge mode", in which the game's difficulty level rises considerably, but most items, including all weapons, are carried through. Bosses, which are a mainstay in the series, are featured in some levels. Racing, in the form of hoverboard races, and aerial combat missions, in which the player controls a spaceship, also appear in the game. Skill points, which were prominent features in the previous games in the series, do not return, instead substituted by the PlayStation trophies system. Several collectibles are present, such as holocards, which provide information about the world, and gold bolts, which unlock aesthetical extras. Gadgets are automatically equipped at certain points in levels, weapons must be equipped manually, and lastly, the OmniWrench, which acts as a melee weapon, is always equipped as it has a dedicated button. Items are used in several different ways. Crates also contain health and ammunition. Bolts, which are found in crates, dropped by defeated enemies and given as rewards, act as currency. The player unlocks weapons and gadgets as the story progresses, but some are bought through vendors. Aside from battling enemies, the player utilizes a Swingshot to cross gaps, rides grind rails to travel through levels, walks on magnetic surfaces, activates switches to open new paths, and occasionally must solve a hacking mini-game. New planets are unlocked once story objectives on previous planets have been completed. The player progresses through the story by travelling from planet to planet. Environments are presented in a somewhat linear manner, although multiple paths are available for the player. It features new weapons, such as the Pixelizer, which gives enemies an 8-bit appearance.
Though Ratchet & Clank is a re-imagining of the 2002 video game, it has a variety of gameplay elements from different entries in the series, such as strafing, automatic weapon and health upgrades, manual Raritanium weapon upgrading, and the inclusion of weapons seen in later games. Clank's gameplay sections mostly revolve around solving environmental puzzles, rather than defeating enemies. Clank is not equipped with weapons instead, he utilizes punches to defeat enemies. Clank's gameplay sections are drastically different, even though the premise of navigating environments and the controls remain the same. Clank is attached to Ratchet like a backpack, performing several functions, such as allowing diving in water, gliding through the use of propellers, and on occasion, acting as a jetpack to allow flight. As Ratchet, the player navigates diverse environments, defeating enemies with an array of different weapons and gadgets, and traversing obstacles. The main playable character is Ratchet Clank is playable in several portions of the game.
Ratchet & Clank shares many gameplay similarities with the other entries in the series. This gameplay mechanic was first featured in the original game. In Ratchet & Clank, players can use the Swingshot to grapple targets and swing across gaps.