In v1.3 There's also an xmen feature adjustment on the menu for "NC mystery progression enabled", or something like that. It's default is "No". Switching to "yes" makes NC mode the third Blackbird scoop reward.
Otherwise, like everyone said, you get it for competing three hero modes and for beating a villain after completing at least three hero modes, I believe.
NC mode rewards an extra ball for the first completion , and around 6mil or so every complete after that. NC mode after the hero modes and after the villain completion after three hero modes count as two separate modes. So you can get an extra ball for the hero completion NC mode AND the villain completion.
NC mechs are used also, as stated previously, during Rogue, Xavier (only if NC is the "mystery" mutant.....some mystery) and are also used during the Danger Room wizard mode to represent gun turrets and "shields" to block shots.