Tools of Destruction retains much of the basic gameplay found in previous Ratchet & Clank games, the game being primarily a shooter-platformer. The player controls Ratchet most of the time, with some sections using Clank, as they explore various worlds to complete missions, using Ratchet's wrench and other exotic weapons gained during the course of the game. At times, Ratchet may enter free-fall, or with an upgrade to Clank, will be able to fly; during these periods, the player uses the tilt functionality of the SIXAXIS controller to maneuver Ratchet. The tilt-sensing abilities of the SIXAXIS are also used to control some weapons and gadgets.
On occasion, Cronk and Zephyr (and Talwyn on the latter two and after breaking her out of Zordoom Prison) accompany Ratchet and fight alongside him. While immune to damage, their weapons are far less potent than Ratchet's. Tools of Destruction is the first game where Ratchet, Clank and other characters converse with one another with lipsynced dialogue during gameplay, outside of cutscenes. In various stages of gameplay, Talwyn, Qwark, the Smuggler, Cronk and Zephyr also contact Ratchet by comlink. As with Going Commando, Up Your Arsenal, Deadlocked and Size Matters, there is an arena gameplay area, called the Imperial Fight Festival in this installment. The player also has the ability to pilot a ship against enemy forces in certain levels, similar to those in previous installments; however, the free-flying controls were changed to more of a rail shooter-style experience, and upgrade options for the ship are not present.
At times, the player will control Clank in a mode similar to previous games, using beings of pure energy called Zoni to fight foes, remove debris or reconstruct bridges, and to power devices in the level. Clank possesses the ability to slow down time as well during these sections, allowing him, for example, to make his way under a rapidly closing door as well as levitate.
Weapons gain experience as previously implemented in the series, but in addition, the player can collect Raritanium crystals and use them to upgrade the weapon in additional ways beyond the experience path; weapon improvements are presented in a tree-like structure and require that all previous upgrades be obtained for that weapon first before later upgrades can be purchased. The recurring R.Y.N.O series of weapons make an appearance in Tools of Destruction with the R.Y.N.O IV, which can be obtained by collecting thirteen Holo-Plan fragments hidden throughout the game.
In addition to weapons are items known as ""devices"". While they are selected and used similar to weapons, they may or may not directly damage foes but instead provide an effect beneficial to the player. The ""Groovitron"", for example, is a disco ball that causes all foes to dance for a brief time, allowing the player to deal with them while distracted. The carrying capacity of such devices are generally very low (2 or 3 units for each). Device vendors in addition to weapon vendors can be found in the game, and device ammo can be found in Raritanium chests, although these are usually hard to find.
Armor can be bought from an armor vendor on certain planets. Each upgrade to the armor decreases the amount of damage the player takes from enemy weapons. Each armor upgrade costs a large amount of bolts.
