A native of Rochester, Minnesota, Mallon began producing television and comedy movies while still in high school, and continued while attending the University of Wisconsin–Madison.
Mallon also produced and directed programs for CBS and PBS affiliates WISC-TV and WHA-TV in Madison and made his feature film debut in 1987 with Blood Hook, distributed worldwide by Troma, Inc.
In 1986, Mallon became the production manager of a new independent UHF television station, KTMA, in Minneapolis.
In 1988, Mallon met series creator Joel Hodgson and Mystery Science Theater 3000 was born.
Mallon later directed Mystery Science Theater 3000: The Movie, released by Gramercy Pictures on April 19, 1996.