Plot
The game starts with Superman and Batman foiling an attack on S.T.A.R. Labs by robots controlled by Brainiac. After Batman and Superman defeat what they think is Brainiac, they discover that they have merely been diverted by a duplicate while another has raided the vaults of the Lab, taking Kryptonian DNA and a chunk of meteorite. Meanwhile, Zatanna and J'onn Jonzz (the Martian Manhunter) face off against Queen Bee and her drones, who are being assisted in their gradual conversion of Metropolis by some of Brainiac's robots. After Metropolis has been saved, the League responds to a series of attempted nuclear missile hijackings; firstly, The Key attempts to hijack a missile before he is subdued by the Flash and Green Lantern (John Stewart), followed by an attempt by Killer Frost which is foiled by Zatanna and Wonder Woman. Despite the League's efforts, one missile is launched undetected during a worldwide communications blackout caused by Brainiac.
However, the League realize it has been upgraded; capable of breaking Earth's orbit, the missile has actually been fired at Mars in an effort to free the White Martians, who will invade Earth upon being rewoken. Superman and J'onn J'onnz travel to Mars to stop them from escaping; but this has been yet another diversion from Brainiac who, anticipating their success, took the opportunity to steal vital equipment from the White Martians. Brainiac has also freed Gorilla Grodd from imprisonment, who intends to take revenge on his jailors and humanity with use of his Earthquake Machine. While Wonder Woman assists Superman in stopping the few White Martian vessels that managed to escape Mars and J'onn Jonnz returns to the Watchtower, the rest of the League (including any unlocked characters the player may have accessed by this point) work together to stop Grodd. Alone on the Watchtower, J'onn is ambushed by Doomsday who takes him prisoner and takes over control of the Watchtower while Brainiac steals a Mother Box from the League's vaults. Regrouping in an emergency bunker, the League manage to retake the Watchtower, free J'onn and defeat Doomsday, before confronting the real Brainiac in his.
Seemingly defeated, Brainiac suddenly returns to life as the Mother Box he has stolen activates - and screaming, he is absorbed into Darkseid, released from an interdimensional prison created by a Sensory Matrix Field Generator, who has been manipulating Brainiac all throughout. Confronting the League, Darkseid - his powers augmented by the Mother Box - sentences the league to his fate by banishing them to another dimension with his Omega Beams all except Superman. He then proceeds to transform Earth into a new Apokolips and holds Superman prisoner in a Kryptonite jail. The dimension the league arrive in is complete with both teleporters to allow them to escape and radiation that will allow them to survive Darkseid's Omega Beams. Regrouping, the League returns to Apokolips Earth, rescues Superman, and Superman defeats Darkseid in his throne room, imprisoning him once again in his interdimensional prison and restoring Earth to normal. In the Watchtower, Batman informs the others that if a danger like this should happen again, they would be there.
There are an additional 4 supervillains unique to the Nintendo version of the games: both the GBA and DS versions feature Circe and Zoom, while the DS also includes General and Prometheus.
Read more about this topic: Justice League Heroes
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