The story is about Ratchet Shooter to search for a kidnapped girl.
Commando of Ratchet Shooter space combat is present. However, this time, the player controls Giant Clank, rather than a ship. Also, there are arena battles, but this time, the player plays as Clank in a variety of vehicles. Clank returns as a playable character, and is again able to control a set of Gadgebots, smaller robots which can perform certain tasks for him, although this only occurs in one section of the game. But the player may still play with Gadgebots in Clank Challenges.
This game contains a variety of weapons which can be upgraded. For example, the Lacerator is upgraded to the Dual Lacerators. Mods can be purchased for most weapons from Slim Cognito vendors. Some weapons and gadgets from previous games appear, such as the Hypershot, Bolt Grabber and R.Y.N.O. Nanotech (health) can also be upgraded. The main way to beat enemies is firepower, so bolts (which are used as currency) are an important criteria of the game. Although there is no way to access weapons, etc. from previous games, additional skins can be unlocked on Secret Agent Clank if the player has a Size Matters save.
There is also a new system for acquiring armor. Instead of buying armor from special vendors, as with games such as Going Commando, parts of armor are found in levels, and can be combined to make different suits, each with their own unique advantage, as well as additional protection.
When the player completes the game they can choose to enter "Challenge Mode". Challenge mode is a harder version of the game, with tougher enemies. To counter this, all weapons, armor and bolts acquired so far are carried through. New sets of armor are available in Challenge Mode and there is a bolt multiplier feature included. Weapons can also be upgraded further by purchasing "Titan" versions.
There are a total of twenty-five Skill Points in the game, which are gained by performing certain tasks, the only clue to which is the name of the particular Skill Point. These will unlock cheats in the game. There are twenty Titanium Bolts to be found which can be used to buy skins for Ratchet.