Marathon Short
Released in 1994, Marathon follows the security officer fighting back a superior alien threat in the Pfhor(Four). A simple premise at first, but dealing with your onboard ship AI Durandal complicate matters.
With the Pfhor as a slave empire, the enemies vary from foot soldiers, to insects, to machines. The cyborg S'pht are the most variable. All have flight, take multiple hits and can shoot but some can cloak or have homing shots.
As the father to the Halo series, there are so many similarities that some theorise that this is the same universe. AI, Rampancy, green armour of the security officer and wide use of terminals all point to the heritage.
Marathon is one of the most polished sprite based FPS games that I have played. Puzzles are rewarding, but at times frustrating, as a mistake can mean significant backtracking. The atmosphere is dark, and the fact you can only save at certain points brings tension.
You can download the game yourself from https://alephone.lhowon.org/.