Hi,
the game I'm searching for was running on Win95, could have been a DoS game though.
After starting the game, you were in your base and were able to choose a vehicle from one of the four hangars (if I remember correctly). After choosing your vehicle, there was a cutscene of an elevator showing that the vehicle you've chosen was brought to the surface and the actual game started.
The game itself was 3D, of course, and your goal was to keep away enemies from your base. In case they attacked your base, you would see a message "Base under attack" and you would have to fly back and defend it. It was also possible to land in your base and choose a different vehicle. The game was still running in the background while you were in your base, i.e. it could happen that the base was suddenly being attacked while you were in it and you had to start immediately.
The gameplay was similar to Battlezone and in fact it could have been some kind of mission in it. I was very young back then, so I cant remember if that was just a single mission that I've failed and failed again or not. The important difference to Battlezone was, though, that you were (as mentioned above) able to land in your base.
Thanks in advance!