As I know of it.. SH3, as well as the follow ups to it.. are hard wired aka hard coded, that after so much damage is accrued, that the crew can do nothing to repair that damages... as I understand it.
It may be that you can see if you can make it back to base & end patrol. This should allow for the docks to affect repairs & make your sub sea worthy yet again & then be able to put to sea once more... hopefully.
Or it could be that you are unable to reach home port to do so... thereby having to abandon ship or lose the ship completely.. in this case, if you don't have an abandon ship mod added in... then inevitably, the end result would be the loss of the career then.
I do know that there was an addition to h.sie that allowed for it to be set to abandon ship. Can't recall what the process was, right off.. but do remember that stiebler & rubini... 2 subsimmer's... worked on doing a mod just for that purpose.
Again... from what I know of, stiebler did finish theirs... as for rubini's... no idea if they ever did finalize their mod idea.
Info on stiebler's mod, can be found here:
https://www.subsim.com/radioroom/sho...d.php?t=184951
Info on rubini's, can be found here:
https://www.subsim.com/radioroom/sho...d.php?t=196978
Hope this info helps...
M. M.