I don't want to put in the effort of making another bad history thread for Extra Credits. Just keep in mind the accuracy of their production, especially of history not in the anglosphere, is not very good.

The northeast were not aligned with the bakufu. The bakufu was done, if not before the war started then definately after Edo's surrender. The northeast domains initially came together to beg for mercy for Aizu. Aizu had already sent message swearing loyalty to the new government and asked for leniency (though they didn't surrender). Unfortunately, the new government has absolutely no plans on forgiving Aizu. It could be that Aizu, as Kyōto Shugo had been one of the biggest enemies of Chōshū and dealt them the greatest damage on the ground (except maybe Satsuma, back when they were on the bakufu's side). It could be that Aizu was just that fighteningly effective in the bakumatsu and the new government did not want any possibility of a powerful resistence. It could be they wanted revenge for being beaten again and again in the bakumatsu. It could be any combination of the above. In any case the new goverment had absolutely no plans of sparing Aizu (at least not without a surrender, which Aizu being just as hot-headed wouldn't) and rejected their request. Sera Shūzō of Chōshū Domain was sent to the northeast domains to get them to attack Aizu. There, he found the northeast still harbouring pro-Aizu sentiments. Sera wrote a memo to pass up to the Edo, saying the entire of Mutsu and Dewa were enemies and suggested attacking them by force. The memo somehow fell into the hands of local samurai, who assassinated Sera. From there it was surrender and be punished, or resist and lose and be punished. The northeast chose to resist.