The Vague Game

Penguin Land?

EDIT: nevermind, I'm an idiot.

bVork got it.

To defeat the mechanical menace, you must become it.

That could be any of a huge number of games, but I'll bite.

Quake 4?

Nope. No biomechanical stuff here. It's all robots.

rise of the robots.... 2

Nope. Pay attention to the latter part of the initial clue. It is quite literal.

Rez?

Nope. Much, much older.

Further clue: It takes place on a fleet of eight spaceships.

System Shock?