Jonathan had heard about the outer heaven uprising in 1995 as did the Zanzibarland takeover through normal news channels but was nothing more than a bystander- and outsider to what was going on behind the scenes as he continued his policenaut training.

Beyond Coast was never fully completed during its construction in 2005 (Partially due to budget cuts and money being ultimately diverted to military projects from then president George Sear's administration) resulting in Jon's talents as a policenaut never being realized therefore he was never plunged into the darks depths of space by 2010.

By 2009 He would continue his career in law enforcement and would eventually find himself working as a private investigator.

Jon's only lead in his wife's disappearance was a book she left behind at the scene of her abduction, a book title In the Darkness of Shadow Moses.

He does make contact and interview with the book's author Nastasha Romanenko but in doing so Jon inevitably finds himself in a rabbit hole of conspiracies and political intrigued resulting in Jonathan becoming a target for the shadowy government known as the Patriots.

Make them angry, scare them, or make them sad. Give them a shock or brighten their day. Fluster or frustrate or infuriate, it’s your call. 

People give Kojima a lot of shit for goofy plots but conveniently forget he basically called most of the last 5 years way back in 2001.