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Rip it all out (see photo above)!
The joists are watermarked but seem solid - the rot seems to have been exclusively in the additional timber at the front, apart from the mouldy patch of ply bottom left - not sure whether to leave, treat or cut out.
I’ve had a board (bog standard chipboard) up and underneath has some weird black dust/mold on the plasterboard below but that seems to be the extent of it.
Dramatic_Hammer-
I'd strongly recommend a shower tray over titting around with wet-room tiling. Our "wet-room" floor failed because the ply that it was laid on was not thick/stiff enough. It flexed under the weight of anyone using it, which cracked the grout, which allowed water through, which rotted the ply (despite tanking). After I ripped that all out I "sistered"some level extra joists to the existing (slant-cut) ones, added loads of noggins and then re-boarded the floor with marine ply, which I painted with tanking paint before putting down the cement base for a shower tray.
The only pain was attaching the new drain, since I had no access underneath. I just had to set up the drain really carefully and pull it up as I screwed the top collar into it. The wall tiling was mostly sound, but where the walls needed sorting I used cement board (take not of the instructions as it can be nasty when you cut it). If I needed to do the walls I'd definitely use panels instead of tiling. In general, the fewer joints the better.
ffm
It was at this stage of my shower replacement that I found out that the previous builders had created the fall on the shower by carving a sloping piece off the end of each joist.
Which bits are rotten and what's your overall plan there?