Much like every episode of the television series, every level of the Wii version of the video game begins with Batman having a battle against a teaser villain. The only ways the levels of the DS version of the game play as if they were real episodes of the show are that each level has a title screen and, like in the Wii version, the characters are voiced by the same people who voice them in the cartoon.
Both versions of the game have Batman team up with another hero to defeat the boss, or villain of the level. In the Wii version, the game supports drop-in/drop-out two-player co-op. Each level has two characters(one of them Batman). Every playable character has several special abilities that are used to beat criminals. They are also both able to summon another hero to appear and defeat all enemies on screen. The game even features animated cutscenes to carry out the plot of the levels and make the levels seem more like actual episodes of the TV Show. The DS version, while sharing many similarities with the Wii version, is drastically different. Here, the only playable character to also appear in the Wii version other than Batman is Blue Beetle. The DS touch screen is used to enable the player to switch between different weapons and switch between Batman and the guest hero of the level. It is important that the player use both characters as many of the levels will have obstacles that cannot be passed by one hero, or requires both heroes to work together. The call-in heroes from the Wii version are replaced by a team-up attack. To activate the team-up attack, the player has to work up a combo by attacking enemies repeatedly. When the combo has reached at least 10 hits, an icon depicting Batman and the guest hero in a dramatic position will appear on the touch screen. Tap it with the stylus and Batman and the other hero will combine their abilities to clear the screen of enemies and take away some chunks of health from the bosses. Batman also has a variety of gadgets. He starts the game with a batarang, but gets more weapons by completing levels.
If the DS version of the game is connected to the Wii version, Bat-Mite becomes a playable character. His abilities include dropping health items and power-ups and throwing bombs and anvils at enemies.
Non-playable call-in characters in the Wii version
- Black Canary
- Booster Gold
- Black Lightning
- Red Tornado
- The Flash (Jay Garrick)
- Green Arrow
- Plastic Man
- Captain Marvel
- Hal Jordan
Non-playable call-in characters in the Nintendo DS version
- Black Canary
- Black Lightning
- Booster Gold
- Bronze Tiger
- Elongated Man
- Flash (Jay Garrick)
- Guy Gardner
- Jonah Hex
Wildcat trains Batman in the tutorial level of the Wii version in order to teach the player how the controls work. In addition, many other characters that have appeared on the show appear as non-playable call-in characters in the Wii version. Also, if the player connects the DS version to the Wii version, they can play as Bat-Mite. In the regular Wii version, Bat-Mite will occasionally appear to give hints to the player. There's also a feature in the DS version called Bat-Mite Boost, where Bat-Mite gives Batman unlimited health and shortens the lengths of pits and chasms, making Batman invulnerable and impossible for him to fall to his death. Curiously, while the Flash is mentioned in the Wii version, he is not a playable character in either (though one of the call-in characters available in the Wii version is Jay Garrick, the original Flash, and that same version of the Flash has a bio that can be obtained in the DS version). Robin also makes a non-playable appearance in the DS version.
- Batman and Blue Beetle are the only characters in both versions of the game that are playable. Some of the call-in characters from the Wii version (such as Plastic Man and Red Tornado) are playable in the DS version. While you can play as a Green Lantern in both versions, you play as Guy Gardner in the Wii version and Hal Jordan in the DS version.
- The only villains that appear in both versions of the game are Catwoman, Gentleman Ghost, Gorilla Grodd, and the Clock King. Interestingly enough, Catwoman's levels in both versions of the game take place in Gotham City, and both the Wii and DS versions of Gentleman Ghost's levels are in London.
- In the DS version, most of the bosses appear to get killed after they are defeated(e.g. Babyface seemingly plummets to his death when he is defeated, and Clock King is presumably crushed to death by the clock behind him)
- Gentleman Ghost's level in the DS version of the game bears many similarities to the episode Dawn of the Dead Man!(Green Arrow is the guest hero, Deadman's bio can be found, and Gentleman Ghost rides on a skeletal horse. The level even takes place in London)