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The Alpha Squad is an elite squad that appears in Mech Mice Genesis Strike. They confronted the Genesis Squad when Ziro found the artifact to steal it from him. Their commander is Nitro, Ziro Federink's stepbrother. Little is known about the squad, aside from Magenta being the previous lieutenant, and two grunts; Ragtail and Boggs.

After the Alpha Squad arrests all members of the Genesis Squad, they go into the Dark Union's Hive to capture who they think is Colonel Black on the run. Instead, they are confronted by a massive bug, killing all but two of their squad. The Genesis Squad escape and go into the Hive, only to find the three charred Alpha Squad members. Ziro is able to watch Ragtail's last message on his communicator, which shows the bug picking off the mice one by one.

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