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, sky diving, flying, and many other things during the course of the game. In addition to the base formula, this adds a main hub in the form of the starship, Phoenix, where you can play Qwark vid-comics (explained later), train, buy weapon and armor upgrades, and change the appearance of your spaceship.

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 and ammo. Weapons will also level up automatically (and gradually) the more you use them, resulting in increased fire power and new abilities.

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 door opens. Ratchet will also have to use other devices to get through an area; like the Refractor, which is used to bend and redirect lasers, and in turn, open doors. And disguise himself as a Tyhrranoid, then play a mini-game where you match up the buttons on screen in the right timing, which will have them disable force-fields on the other side.

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 (with the quick weapon select menu) like Attack, Follow, Wait—and he'll also have to have a certain amount of them to unlock doors and progress to the end.

In additon to controlling the robots, Clank now has a gun that shoots bananas, which is used to command his monkey side-kick, Skrunch. Clank can use this device to shoot the bananas onto hard-to-reach buttons. Skrunch will then follow the banana, and stand on the button, which will open doors and extend bridges. Clank can also use this to shoot bananas into the path of gun-equipped security spotlights, and let Skrunch distract them, while Clank sneaks by unscathed. Another area has a giant Clank fight on a set of a miniature city (he's filming a movie), while fighting (godzilla-style) with robot ninjas and another oversized monster.

Like the last game, There's one 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 completing an event, you'll earn a set amount of bolts. Other than just fighting enemies, the arena has specific objectives, like beat enemies before time runs out, don't get hit even once, finish the round before you're knocked out by gas, etc. This also adds the arena-like battle mode. These have a missions' select screen, just like the arena, and award you bolts upon completion. However, unlike the arena, the battle mode is integrated into the main game. In these events, you'll compete alongside allied robot rangers, as you fight dozens of enemies, while trying to take back bases and get turrets up and working with your wrench—a couple of these missions also put you in a hovership.

The Qwark vid-comics are available to play in the Phoenix, and are a video game within a game. You acquire chapters of these vid-comic gradually, and play as Qwark through several side-scrolling levels, while punching and shooting enemies, jumping from platform to platform, and then fighting a boss at the end of each level. Completing these missions will also earn you skill points, bolts (the game's currency), and platinum bolts, which are used to unlock the game's extras.