Reaching O-6 (U.S. Navy Captain) generally requires about 21+ years in service IF starting as an officer and being well liked and hitting all the marks, yet it's clear the protag could not have joined as a commissioned officer because he 'signed up' at age 20.
He's 38 years old at the time of present-day gaming. That's not enough time to get a bachelor's degree (3-4 years and required to become a commissioned officer) while on active duty plus two decades of service. In addition, the story says he was discharged for a time because of his handicap (9 months, 1+ years?), making the whole timeline even more implausible, Navy SEAL (I'd suggest not going that route) or not. Then add in the time spent in the apocalypse (another half year or more?). As an aside, nothing about this feels like he was a SEAL, it seems more like dev's 'story example' was but one optional backstory option to explain things, and in fairness, means it's not canon.
Also, it's extremely rare (generally nonsensical) for enlisted or officer to get injured and just *poof* be put into a different and particularly high-skilled occupational branch/specialty without having to graduate in that school. A 'radio operator' Navy Captain (which doesn't exist.. perhaps comms officer), for example, can't just suddenly become a 'strategic analyst' because he got shot. That's not how any of this works. At all. In the civilian world, imagine an electrician having a health issue and then magically being given a job as an attorney.
Also, being an intel guy in no way removes the requirements to be a warfighter or likelihood to be sent into warzones. It's not a magic way to become a desk-jockey with cachet. I happen to have some personal experience in this, FWIW. Nevermind that at that rank (Navy Captain), he's taking on his own command of a navy cruiser or other ship or submarine, or otherwise filling a senior position on a command staff. Commissioned promotion
requires command.
There are far easier ways to accomplish the kind of lore-flexibility the dev's story seems to call for: A former service member who became a PMC (private military contractor) is one example, agency operator (like CIA or DEA) being another. Combat veteran turned mercenary or high-skilled criminal being yet another. Those sidestep the backstory contradictions.
Reasonably, most won't care about these seeming technicalities but I get the sense that the dev cares about such lore so I hope I'm able to provide useful info to support his broad vision.
For the most minimal of changes while comporting with the spirit of the story as I've read it, I'd suggest a former enlisted US navy man who was injured and 'medically discharged', and upon healing was recruited to become a CIA special operator/contractor (because of connections, a particular psych profile, and specific stand-out skills in demand at the time). A generic PMC, DEA agent, criminal, or merc would likely have no reason to end up in Japan for an extended timeframe, but a CIA ops guy offers extreme flexibility to fill in the hazy parts, being a particularly clandestine and unconventional vocation (in other words, a broad opportunity for fictions).
Alternatively, if the protag MUST be a commissioned officer, he needs to be older upon joining the armed forces (i.e., already having graduated with a bachelor's degree) and have a lower rank to fit the age and timeline presented.