Gameplay sum up: The basic formula in every Ratchet & Clank game is: land on a planet, destroy enemies in your way, get to the other end of that planet, watch a cutscene, find out what planet to go to next, and repeat. During these missions you'll mostly be shooting and hitting things, but you'll also be jumping and/or hovering (with the help of Clank) from platform to platform, collecting bolts (currency), grinding on rails, walking on magnetized walls, swimming, hoverboarding, and many other things during the course of the game.

Every level has dozens of breakable crates scattered throughout; filled with bolts, health, and ammo. Enemies also shed bolts when you destroy them, and act as the game's currency for buying and upgrading all of your weapons. All levels have more than one weapon kiosk, which is used to buy new weapons, ammo and upgrade your weapons with new attributes like adding electricity to your rounds, or burning acid to your ammo. Weapons level up automatically (and gradually) the more you use them, resulting in increased fire power and new abilities. And unlike most games in the series, you can't upgrade your armor in a shop. Instead, you will have to find single pieces (as in helmets, boots, etc.) as you progress the game.

The majority of the platforming will be done using Clank. He sits on Ratchet's back like a backpack, and (by the third level) is equipped with a built-in, mini helicopter that comes from his head, which is used to hover over small gaps, and jump extra high to reach normally unreachable platforms. To traverse larger gaps, Ratchet will use the Swingshot, which will grab onto certain hooks in the sky, and swing him to the other end. Other than using it as a weapon, Ratchet will use his wrench to open certain doors, by grabbing onto unscrewed bolts and turning them until the closed door opens.

Sometimes Ratchet will have to use certain devices to get through an area; a good example is the Sprout-O-Matic, which is acquired early in the game. This device sprays a special serum out of a watering can, and is used to sprinkle on certain flowers in many of the levels. When you do this, the flower springs to life and will follow you to specific patches of dirt. It will then plant itself in this dirt, and then either grow itself into a ladder, a launch platform (for you to reach a far away area), or a bomb, which you can then hit with your wrench and destroy walls blocking your way.

A few key moments in the game put you in the shoes of Clank. Clank can enter smaller places than Ratchet, and activate devices to further progress certain levels. Although Clank isn't equipped with guns, he can hit things with his fists and control groups of fellow robots. Clank will use these robots to traverse the area by giving them commands like Attack, Follow, Wait—and he'll also have to have a certain amount of them to unlock doors and progress to the end. There are also a few areas with Clank in giant form, where he flies and fights through space. These levels are on tracks, and have you constantly dodge and shoot the enemy, while trying to collect bolts and escape the area. In addition to these, Clank will fight a few of the bosses in his giant form.

There are two planet that gives you access to the arena. The arena is a place where you can compete in multiple matches, which pit you against dozens of opponents, with a variety of obstacles and objectives. After you complete an event, you'll earn a set amount of bolts, armor, and Titanium bolts (to unlock secrets). However, this time, instead of playing as Ratchet, you compete as Clank in three specific types of games. The first puts Clank in a vehicle, with the objective being to destroy your opponent's vehicle. The second is where Clank is made to pick up a ball, and throw it into the goal before his opponent can take it from him and do the same. And the last is like Lemmings, where you have to direct a group of robots to safety through obstacle courses.

Last of all, there are a few (non-optional) areas in the game where you compete in Skyboard races as Ratchet. These portions consist of racing around a track with other Skyboarders, as you try to make it in first place. Although they're pretty challenging (and can get a bit frustrating at first), they're pretty easy to complete once you've memorized the tracks.