Black Joker of WC in Russia fame points us to a Wing Commander scenario for Master of Orion 2: Battle at Antares. You can play as Human, Kilrathi, Firekkan or Nephilim and the larger ships can carry fighters and bombers. Here's what the documentation says:
This scenario is a contribution to the Wing Commander saga. In future, the Human race is locked in the long-lasting war with cat-like creatures, who call themselves the Kilrathi. They are very agressive and are going to enslave the entire Galaxy. Depending on the side you play, your goal is either to save the future of Human race from the cruel furbags, or show the hairless apes their real place - beneath your foot. Another option is to play the scenario with a friend in a hot-seat game.
You need to have your Master of Orion 2 patched to version 1.31 to play this scenario. You can download The Kilrathi War here. They also have many other downloads including tools, editors and over 30 other scenarios (most notably one based on Babylon 5).