This is the official info. Mind you this is for NGO, but I don't see why the algorithm wouldn't be any different at TYO.
https://www.forth.go.jp/keneki/nagoy...uarantine.html
In short, if you're a gaijin and test positive, you go get medical eval followed by additional medical treatment and/or quarantine at a Covid 'accommodation', then return to the airport upon completion of the treatment/isolation to go through the arrival immigration.