Alright, so after 2 hours of trying every pixel of Cyber Org, I have found a solution to my yesterday's problem.
So, if you are stuck on Watchtower 101 in the room with alarm going off and countless enemies spawning, do this:
1. Pick T.J. as your character
2. When you reach that room, HOLD CIRCLE TO BECOME INVISIBLE
3. Just go through the room, and no alarm will be triggered!
Regards to my curiosity for finding this!
Oh by the way, did I mention that this game kicks ass? IT KICKS ASS!
Here are some keywords to ease the search: psx ps1 cyber org watchtower problem stuck issue walkthrough alarm