Board Thread:Show-Related Questions/@comment-202.78.169.243-20160427142603/@comment-26247132-20160427163812

They addressed that in the first episode when Jaha revealed to Murphy the reason he was locked up for 86 days in the bunker is because Jaha and ALIE had to work on the nuke. They converted it into a mobile power source for ALIE (the backpack we see them carrying around).