Index -> Playing the Game -> End of Turn
After the draw phase, any effects scheduled to happen "at the end" of the turn are carried out, and any effects scheduled to last "until the end" of the turn cease to function.
At this time, each ship with shields that is not in hyperspace regenerates 2 shields. Some cards can modify this amount. (Some cards grant the ability to regenerate hull. This also occurs at this time, even for ships that are in hyperspace.)
Once all that is complete, victory conditions are checked.