Stargunner

"Stargunner is a horizontal scrolling shooter computer game developed by Apogee Software. It was released on November 19, 1996, and it has the distinction of being the last title sold under the Apogee brand name.

In truth there are actually two different story lines for Stargunner, those being the one described in the official playing manual included with the CD-ROM copy and the one which is found on the 3D Realms/Apogee website along with a host of other game review sites and inside Stargunner itself.

Manual story

The huge carrier ships of Barak entered Amdara space with signs of friendship and cooperation. The peaceful Amdarans welcomed them and helped them colonize a nearby planet. But soon after, the masked Barakians revealed themselves as a warring race with conquest in their blood. Now two thousand years have passed.

Locked and beaten down in a staggering war, the Amdarans have one final hope before surrendering to the overwhelming Barakian forces. The Amdarans have trained an elite squad for an offensive strike design to cripple three strongholds on Barak, where the majority of Barak's space fleets are amassed. If the offensive strike team can surprise the Barakians on their own planet and destroy most of their fleet, then hope is not lost for the Amdarans.

The people of Amdara have nicknamed their elite force the "StarGunners".
Website/in-game story

In the far distant future, an epic war for survival takes place...

Deep within the Andromeda galaxy, the people of Zile grow restless--and greedy. The Zilions secretly prepare for a massive strike against the nearby planet Ytima. Fearing such an attack the Ytimians train an elite squad of "Stargunners." Their mission: To strike the planet Zile first, and cripple the Zilions three strongholds, where the Zilion war fleets await the launch order. If the Stargunners can surprise the Zilions on their own planet, and destroy most of their fleet, then good will triumph at least one more time."

Source: Wikipedia, Stargunner, available under the CC-BY-SA License.