It's retired at the end of season one, resurrected and used throughout season 2 but classified and buried at the end along with anything relating to Discovery, the Red Angel timesuit and Michael Burnham. The USS Discovery is flung to the distant future where season 3 will take place, removing the characters from the equation. Presumably, they'll keep using it in the 32nd century. This is entirely unsatisfying as a reason for Voyager and DS9 to not resurrect or reinvent from scratch the spore drive tech to render their distance-based premises obsolete. I was expecting the spore network to be blocked off by the woodland critters that live inside it, or by people on our side. Not just put a Starfleet classified stamp on it and carry on. While I loved the season and it's finale, that part does not cut it.