Like the console version, the central focus of the two DS games is a linear campaign of missions, following basically the same story, split in two parts. Additionally, there is an Arena mode with five "arenas", each with six missions available, four bonus levels from the opposing game, and seven multiplayer levels.
Before each mission, you pick two Transformers from your available troops. During the mission, you switch between the two chosen characters using the A button. If a character is knocked out, they can be revived by defeating a certain number of enemies with the remaining character. New characters can be unlocked by completing campaign and arena missions, locating "data disks" which appear as floating golden discs, or using unlock codes. There are 24 unlockable characters in total, 14 through the campaign and 10 in the arenas. Other data disks can be selected at the start of a mission to boost character stats.
Characters are classed as "Heavy", "Light" or "Air". While "Air" has the obvious advantage of flight, missions contain areas which only certain classes can go: marked walls can be bashed down by heavy vehicles, and there are small spaces where only light vehicles can go. There are also three weapon types: "plasma" represented by a red circle, "laser" represented by a yellow triangle, and "solid" represented by a blue square. Each character has a ranged weapon (typically plasma or laser) and a melee weapon (typically solid). Enemies are particularly vulnerable to a certain type of damage, which is visible as the symbol representing that damage type above the enemy's head. Advanced enemies can change which damage type they're vulnerable to.
While the foes have health bars that appear over their heads, the player has three bars on their HUD — a health bar, an energy bar, which represents energy they can use to fire, and a boost bar which appears while in vehicle mode, which they can use to boost their speed. All three bars will regenerate in time, though for "Air" characters, the energy bar will not regenerate while they're in vehicle mode.
The game also incorporates a leveling system. Characters begin at level 1 and gain experience by killing enemies and finding Energon cubes. Each level gives the character a stat point which can them be spent on one of three stats to increase the character's power. Some stats, when upgraded to a certain level, bestow on the character extra powers, such as new attacks, more powerful weapons, and sundry other abilities. The maximum level possible is 20, giving 19 stat points.
Multiplayer is achieved by using the DS Wi-Fi. Available game types for multiplayer are Deathmatch, King of the Hill, Capture the Flag, and Energon Dash. Additionally, you can play "Ante Games", in which each player bets one of their characters on the outcome. The winner gains the loser's ante character, but the loser can unlock their character again by playing a "rescue" mission, assaulting a prison to free the lost character. Data disks which are exclusive to certain levels available only in the opposite version can be obtained only by playing in multiplayer.