how do you go about working with a teammate that the best thing would be to rewrite the code he worked with for the last 5 months!?

I mean, no separation of concerns, layers upon layers of unnecessary abstractions, unneeded parallelism and mutex and whatnot...

Like, 5000+ lines of code that could be done in 400...

If you didn't exaggerate the severity of your colleague's retardedness, its's not a tricky question: suggest to fire him?

Or maybe, he's a junior and the knowledge gap between you is so great that you forget that you've been there and done that too?
Perhaps you/ your team are purists that set annoyingly high standards?

Maybe the colleague had a background in a different programming language and was left without guidance and didn't have the tendency to ask for help?

The fact you realize only after 5 months definitely suggests there wasn't enough followup on your (teams) part (demo's, milestimone reviews).

Probably a bit of all of the above?

Tried pair programming with them?

I don’t know how to fix this but I know how to prevent this from happening: PR reviews. Nobody should be able to push directly to master except through code reviews.