There seems to be three fates for Jack after he's killed the fat Hydra, if he's not killed in the falling masonry and escapes he'll be confined to an asylum where he commits suicide (I'd rather die heroically in the Deep One's city I think), or if the final score is good enough may join the Yithians on their alien world.
But the thing is I don't trust this Yithian outfit, look what they allowed to happen to the poor guy at the beginning! Their enemies the Polyps may therefore be just getting a bad press from them! Therefore I chose to return from the Temple back the other way via the ventallation tube to the Polyp vault and wait.
Its too vast to be flooded by the sea from the shattered Deep One city and I'm sure the remaining Polyps have the power to seal it off if need be

Its true nothing will happen in the game if you do that, but you can just wait there safely and quit. Poor Jack will either starve to death there, be killed by returning Polyps or perhaps as this diary entry suggests:

The Diary of Jack Walters
Feb 11 1922

Sealed in the City I decided to track back to that deep vault where those monsterous things dwelt, at least it looked safer that deep down.

I made it and waited for hours in the dark depths, until they came.

Feb 23 1922

I had thought I was doomed at first, but utilising this bizarre ability of body switching I learned in the Hydra temple I managed to enter the mind of a Polyp. Communicating with the others I learned they werent really that bad, sure they often had an attitude problem, but so would anyone sealed down there for millennia. Once we communicated and I told them how I [censored] over the Deep Ones and didnt trust those Yithian things, I became a Polyp celebrity. They completely repaired my human body, made it near immortal and activated somekind of hypnotic device that made me see the Polyps as 'hot chicks'. I'm now having a hell of a time down here and as soon as some expedition breaks the sealed doors near Milton Keynes I'll be free again to serve my new Polyp masters on the surface! They told me my sanity would not have survived the escape through the Deep One portal and at best those horrible Yithian things would have captured me and given me an ugly new alien body, no way. I still can't believe the lies they said about these sixy Polyp chicks. I think I'll be happy down here, better to rule in the vaults than serve in the Yithian dreamworld.