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EDIT 2 @Lexible Thanks for an idea. I checked Blindsight and while it shares quite a few similarities, it is definitely not it. But while reading it reminded me, that there may have been something characteristic about the AI in the story, but I can't recall what. But I think I'm recalling it was learning. The first time humans entered its base, AI did not expect anyone to pass outside guarded perimeter, so there were simply no guards inside. Next time it was prepared better and guarded the base from inside too. I think this is also why it was so difficult to beat it. Because every time some surprising tactics almost succeeded, AI made sure it will never be caught off guard like that again.

EDIT:

Thanks everyone for your time so far! It might very well be a fun work. I may have read it on some web page dedicated to such stories. I may have read more of them, but none left any mark in my memory, just this one. I remember it was so well written and had such a dense atmosphere of facing the impossible-to-win fight and losing step by step, that I could not stop reading it. There was for sure some gore scenes, especially the experiments description during the first enemy base exploration. I do not remember much of a violence or to be explicit, probably no sex scenes too. And yes, as far as I can remember most or all of the main characters died at the end of their part of the story. The story itself was split to something like chapters and at least the last chapter has completely different main characters. I believe there were 3 - 5 chapters. The first chapter and maybe more than the first one was about that young pilot and I'm recalling something that it may have been a woman or there was some woman involved in very first enemy base exploration (as a last man standing and the story was following him/her until the ugly death). The soldiers from the last chapter have been mixed men and women for sure, could be a group of 5 or 6 people.

The story was not long though, probably not long enough for a standalone book. I realise that chances to identifying it are little to zero, but it's poking my mind for years, so I decided to finally try the power of community.

Hopefully someone knows this story. I tried to search for it, but the most specific details I can remember (like the bomb) yielded no results. It may be very difficult as I don't know, if this was released internationally or it was just small story in my native language (Slovak or Czech maybe, not really sure, but my English was not good enough to read a story back then).

I'm not sure, if I'm not mistaken by some other story or movie, but I recall very weakly, that the AI core room was described like sphere like room just big enough for an adult man standing and full of backlighted tiles or other lights perhaps changing colour and intensity as AI was speaking or thinking. But I may be completely wrong, unfortunately.

Hopefully someone knows this story. I tried to search for it, but the most specific details I can remember (like the bomb) yielded no results. It may be very difficult as I don't know, if this was released internationally or it was just small story in my native language (Slovak or Czech maybe, not really sure, but my English was not good enough to read a story back then).