One of the most prolific screenwriters in the action/adventure genre, Jonathan started his career writing episodes of The Young Indiana Jones Chronicles (1992) for George Lucas and ABC. He wrote Die Hard with a Vengeance (1995), re-conceived from his original spec script "Simon Says". He followed that with Jumanji (1995). His script for the The Saint (1997) was completely re-written by others. After this frustration, he enjoyed a long working friendship with producer Jerry Bruckheimer with whom he collaborated on many projects since 1996. He re-wrote the whole script for The Rock (1996) without credit, which he tried desperately to achieve via WGA arbitration.

He did uncredited re-writes on Con Air (1997) and the remake of Gone in Sixty Seconds (2000) and received executive producer credits on both. Armageddon (1998), from Jonathan's original idea, was the second time Jonathan had the highest grossing film, worldwide, at the box office. The other was Die Hard with a Vengeance (1995).