Sorry, I missed one more critical detail there… This game was in space! Played on a 2D, wraparound surface, with a top-down perspective, but it was definitely in space.
The fighters were fast and cheap but weak and could only shoot lasers.
The bombers were slower but tougher and could fire missiles. (Missiles could also be scripted, come to think of it. And if you made them stop, they turned into mines)
The fleet ships could manufacture other ships. You only have a single fleet ship at the start, but as time goes on, you can build more. …if you haven’t spent all your resources on building fighters and bombers.