It is story based, and can't be missed.
The Tormenter is very easy to take care of though, initially he will fall from the ceiling of a huge room you walk in, and start dragging you with his tongue. On his body, you will see a part that is yellow. You will need to shoot this 4-5 times in order for him to retreat. I don't think he can hit you in this part (?), so just relax.
The second encounter with him comes just after Isaac has fallen down a chute in a cutscene. He will grab you, and although the game will still be in cutscene mode, you will have control of your weapon. Shoot whichever part of him is bright yellow again, you will have to do this 4 times. He then releases you, but you must be quick to use your Kinesis on the door blocking your way.
As for the final part, you must shoot one of the explosive tanks flying off the ship you're both clinging to. This will propel you into chapter 6 along with getting this achievement.