Ironseed

Originally released in 1994, this is the rewritten-from-scratch 25th Anniversary Edition!  The entire game has been recreated using a modern 3D engine to be as faithful to the original as possible.... 

It is the thirty-eighth century.  The fall of Earth is but a legend and humanity has migrated to a terraformed Mars.  The Pentateuch, a group of five priests, rules the newly risen technocracy with an iron fist.  In a bold attempt to eliminate the last of their political opponents, the five began the purgation trials.  With guerrilla tactics their followers went about convicting those who would oppose them.

To counter them an underground movement was initiated and an elaborate plan was conceived.  A virus was spread throughout the circuit matrix.  A thousand days from inception, the virus was scheduled to delete all personality files.  The Ironseed Movement, as it was called, hoped that by stealing a ship they could escape... leaving behind Mars... and the Pentateuch.  Their intent was to return after the fall of the technocracy. ...but a computer malfunction turned a thousand days into a thousand years...

As the captain, you are awakened along with the crew by an alien horde.   After a brief dialogue, communication is cut off and they attack. The game begins as the attack ends. 

Homepage - http://ironseed.net

Wikipedia - https://en.wikipedia.org/wiki/Iron_Seed

Original Game Manual - http://ironseed.net/ironseed-manual.txt

Reddit - https://www.reddit.com/r/ironseed/