Inspired by Searching for video game like Xevious but with more interesting bosses, I'm resuming my search for a video game I played once or twice sometime around 1990, at an arcade in Salisbury Beach, Massachusetts. I made a strong effort to track down this game 10-15 years ago without success.
The graphics were very reminiscent of Time Pilot '84, and like that game it was all-direction scrolling shooter.
You piloted a small spaceship and were trying to destroy a large thing, either a base, or a large ship or creature (I think it had a somewhat organic look). The base or whatever was flying or hovering over the ground, which may have been a barren moonscape, but I might be mixing that up with another game.
The interesting thing was that the 'base' or whatever was sort of a 'network', consisting of nodes branching to other nodes. Some of these were just worth points while others were weapons that fired at you. If you managed to fly in 'deep' (your ship was 'higher' than the base thing) you could destroy a parent node and all the child nodes would explode too.
I believe there were also flying enemies that attacked you while you tried to do this. I don't remember whether your ship had more than a single weapon - there may or may not have been another weapon used against the 'nodes' rather than the flying enemies, like Xevious or Time Pilot '84.
It does have some similarities to games like Boskonian or Last Mission.