Used each time you initiate combat. Players can store up to 60 energy. One energy refills every minute.
It seems that the energy refill rates vary from 1/4/5 and 6 minutes. The initial guess of the player community that it might be linked to the Commander level, but after several discussions with other players who are on different levels, the experience shows that there is no direct connection between the refill rate and the commander level. The refill rate differences might be a bug as far as we know, so far no official statement has been made by the developers.
Energy refills over time
Full refill with level up.
Allies may gift you energy