Just before the end slipgate, look over the edge. There is a ledge, leading to a goodie. You may need it.

This is not a secret, but it usually create some confusion.

You cannot kill Shub-Niggurath with any weapons. You have to do it by hand. See 'Spikey' flying around? Wait until he enters the body of ol' Shub - then jump into the slipgate: you need to telefrag her.