It can be done anytime.
During any mission some aliens will board your ship. Let them start shoot and repair the parts. Don't repair the reactor that is behind the mechanic. It has 3 health bars. When all 3 are gone it will appear a message that it's gone subcrittical. Then repair it. The alliens that are on the ship I found easier to vacuum them to space to get rid of them. Or shoot them with rifles. Easy G it takes some time for alliens to coordinate and shoot the reactor.