How about a time travel TBS?
It seems like a normal TBS, you have a main commander unit who if destroyed ends in you losing the game, he also for all intents and purposes exists "outside" of time. Essentially he can teleport himself and a few units around in time at a massive cost, this sends the units back in time and begins a countdown clock ticking. Call this clock temporal resistance or something and it goes up the more distorted the past becomes, once it hits a threshold the time travelling units are thrown back to the original turn. Once you return to the present it is different based on the changes you made. I think maybe an example is needed to clarify:
It is turn 300 and the enemy is pumping units of bas F, base F was built a in turn 250 and lightly guarded until new technology allowed the enemy to turn it into a massive production facility. I could try fighting to take the base and destroy it but instead I send my commander back with 5 of my most powerful units (At extreme cost of course) to turn 250. The enemy will now act exactly as it did during those turns last time, all of my units will too and I only have control over my commander and 5 units. I move to the now lightly guarded base and destroy it. Every turn I am here my temporal resistance grows, if I stand on a square an enemy tries to move into that enemy then engages in combat if I damage/destroy it that is calculated forward, that unit now no longer attacks one of my units and it now doesn't damage that unit so that unit is now still there when the enemy tried to attack my base and as a result my base isn't captured etc etc. The bigger the impact of an action the more temporal resistance it creates. In the above example I would almost certainly be catapulted back into the future after that combat. If on the other hand the enemy ship I destroyed would otherwise have sat out its life gaurding some remote base then I would only minorly raise my temp resist. Anyhow so if I do take down the enemy base which was my reason for coming back then I am thrown forward to the future and all the units that base made are now gone any units they destroyed are were they were when they were destroyed etc etc.
Minor journies would be possible and much cheaper, for example popping back 10 turns to defend a base from enemy attack, or to salvage what was originally a embarrassing failed assault. Commander units would exist only in ghost form when you go back, touching them means getting thrown immediately back into the future and having any changes you did make reverted. This means they are extremely important for to time immunise units/places but the flipside of that is that you don't want to send them anywhere too risky less they be destroyed.
Hmmmm, this would probably be quite processor intensive as it would have to forward calculate the effects of your actions anytime you did something in the past to see whether its time to throw you back to the present. Also this may be worded poorly/confusingly.