Maybe Mario got kidnapped by the revolutionaries, brought to their secret brainwashing chambers, and turned into a Communist? Then Luigi would have to rescue him again.
Actually, it might not be too hard, suitwise. Mario already wears some red, and wields a hammer sometimes. They'd just have to get his old overalls and a sickle, and make him the second-to-last boss. Maybe Bowser could be an ally, because his army converted to the enemy cause?
Of course, since this is Nintendo we're talking about, they would never do something like this.