Perhaps the game automatically saves at certain points? and you select a ship and click on a century and that ship gets transferred into the saved game, e.g. USS Relativity decides to travel to the 24th century and observe a war. Also the Future Ships will need some kind of ultra powerfull cloaking device (Temporal or Phase Cloak?) or you could decide to change history :O and when your game gets back to the 29th Ce you could travel back again to stop the interference (endless re-playability), sounds complicated i know