secret rooms are pretty easy if you backtrack:
1. try leaving the time accelerating lever in the on (upside down) position, then backtracking to the cliff area.
2. try plugging in the connector to the rusty portal at the cliffs
3. at the area where you get the cube put in this as the ID code
00000
01110
01010
01110
00000
then search around to the left of the ladder pipe and keycard slot
4. put the two wheels in the ladder control room in the down position then backtrack into the pipes.
5. after unblocking the protocols, go back to the first place you plugged the connector in.
Those are the ways that you can find the 5 secrets in the game, good luck :D
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 "Heavy Weapons"){kind=icon}