Fusions are evil versions of the Cartoon Network characters in FusionFall, with green-tinted skin (caused by the Fusion Matter in their body) and glowing red eyes. They were created by Lord FusePlanet Fusion's leader, and modeled after the heroes of FusionFall. They are usually the head of one of Fuse's nasty plans. Defeating them is required if one wishes to acquire a Nano, though not every one creates a Nano. Sometimes a Fusion of a certain character will create a Nano of another one; Fusion Coop creates Megas, Fusion Grandpa Max creates Four Arms, Fusion Ben creates Swampfire and Alien X, Fusion Scotsman creates Demongo, Fusion Tetrax creates Humongousaur, Fusion Demongo creates Aku, Fusion Hominid creates Titan, and Albedo creates Rath, with him being the only NPC fought to receive a Nano. The Fusions to provide more than one Nano so far are Fusion Bubbles, who not only gives out her own Nano, but the Johnny Bravo Nano as well; Fusion Finn, who gives out the Jake Nano as well as his own; and Dexter, who gives out an Unstable Nano through missions and by creating a Nano from a machine.

Like Nanos, Fusions are created by means of special items that are dear to the character they are based on. Some Fusions may deviate from the personality or physique of the character they based on; for instance, Fusion Bloo is gigantic and vicious, while Fusion Wilt is robotic, like Wilt's imaginary alter-ego, Lord Snotzax.

Normally, Fusions are located in the deepest part of the lair or at least close to it, but there are exceptions. In FusionWilt's Secret Lair, Fusion Wilt is in the first room the player comes to (though this is more likely the result of a programming error with the portals); moreover, Fusion Mayor's Secret Lair has the Fusion in a cavern right next to the entrance, though defeating him doesn't count until players defeat the monsters in the caverns in front of players.

Sometimes an NPC will be inside to pick up items players have found, give them information, or even fight alongside them. (Note that they only fight up to some point and then stop, usually at an item, after the defeat of a certain number of monsters, or at another NPC.) They will be a part of a player's group and will walk blindly in a set path, attacking any monster in their way or nearby. This occurs only with Eduardo, Billy, Professor Utonium, and Grim.

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