The concept of the Pilgrims, a breed of human that possessed a natural ability for space navigation, was created for this film and hadn't previously been mentioned anywhere in the Wing Commander franchise.
In an interview, Freddie Prinze Jr. discussed his hatred for Wing Commander (1999), stating: "I can't stand Wing Commander. I can't watch one scene of that movie... I read the script and loved it. So did my buddy Matthew Lillard. We both got the parts. We went on location and they said, "Here's the new script." It was a piece of sh-t."
The voice of Blair's fighter's onboard computer Merlin (listed as "?" in the credits) is Mark Hamill, who previously played Blair in the computer games Wing Commander III: Heart of the Tiger (1994), Wing Commander IV: The Price of Freedom (1995) and Wing Commander: Prophecy (1997) and also voiced him in the spin-off animated TV series Wing Commander Academy (1996).
Jürgen Prochnow and David Warner had previously appeared in Privateer 2: The Darkening (1996), a spin-off game from the Wing Commander series, directed by Erin Roberts, brother of Wing Commander creator Chris Roberts.
There is a poster of Sarah Michelle Gellar in Freddie Prinze Jr.'s room; they met on the set of I Know What You Did Last Summer (1997) and married in 2002.