Wheatley will make another appearance. Shoot a portal onto the wall behind him and drop into the orange portal.
After he talks for a while, he'll say that he needs to detach himself from the rail and you need to catch him. I've never successfully caught him, but anyway, he'll count to three but then decide that it's too high, so he'll count to one instead. Catch him if you can, but if not, just pick him up.
After a moment, a panel will open on the wall near where Wheatley fell, so walk over to it to put him into the panel. Turn around when he asks you, then a panel will open on the wall next to him. Pick him up and go through the secret panel.
Follow the path. There aren't any threats along the way so just keep going until you get a loading screen.
In the next area, Wheatley will tell you that you need to go through "her" chamber. Go on ahead and you will find none other than GlaDOS, lying inactive on the ground. Continue through the chamber, past the incinerator where you dropped GlaDOS's personality cores so long ago.
Continue on until you reach the main breaker room. Wheatley will tell you to look for the escape pod switch. Look around, but it doesn't seem to be there. Eventually Wheatley will ask you to plug him into the panel that opens up, so do that. He'll do some computer stuff and the platform will be raised a couple of times.
You'll end up back up near GlaDOS. It seems that Wheatley has accidentally reactivated her. She'll wake up and crush Wheatley, then she'll drop you down the incinerator shaft.