On the back cover of the CD-ROM, in one animated cut-scene, and the villain to defeat at the end of Mission IX. He flies around and fires rockets at you. When you defeat him, he flies away.
Game walk-thru FAQ by Game FAQs / Dr. Karsten A. Loepelmann:
Mission XI: The Imperial Mask
In the Computer Core there are two switches: first hit the one at
(0924/66.0/-262), then the one at (0925/66.0/-238). Head west; press
switches at (0853/44.0/-233) and (0852/44.0/-268) to reveal a switch at
(0858/44.0/-250). Take the data tapes at (0860/44.0/-239). The door behind
you (0827/44.0/-248) will open. Follow the tunnel, then head northeast. Go
up the elevator, then north to your ship—which is gone! Then, to quote a
certain former smuggler: "Boba Fett!? Where!?" :) Shoot down the bounty
hunter, and Jan will return.
He appears at the end of Mission
XI, flying around you, shooting rockets.
The number of shots taken to kill Boba Fett is also difficult to
measure, partly because he is hurt (an indeterminate amount) by the
explosions from his own rockets, but mainly because the explosions
blind Kyle, making it difficult to see whether a shot has actually
hit Boba Fett as he dodges about. (It is possible to confine him
horizontally, but much more difficult to prevent him making small
movements up and down, and to a lesser extent also to the sides.)