Master of Orion II: Battle at Antares (1996)

Long before the time in which the game is set, two extremely powerful races, the Orions and the Antarans, fought a war that devastated most of the galaxy. The victorious Orions, rather than exterminate the Antarans, imprisoned them in a pocket dimension before departing the galaxy, leaving behind a very powerful robotic warship, the Guardian, to protect their homeworld.
Some time after the game starts, the Antarans, having broken out of their prison dimension, begin to send increasingly powerful fleets against the players' colonies, to destroy them rather than to invade. The only way they can be stopped is to carry the battle to their home universe through a Dimensional Portal.