I have the same issue. I've gotten to the end of the last level multiple times, but Dr. Fetus doesn't show up. Once I made it to the small bridge control room on the right and the second set of saws eventually moved forward and passed right through me. Then Dr. Fetus showed up and shot a rocket at me which hit the wall but I still died. The second time the second saw blade wall killed me as I was standing in the small bridge control room.
So... you're probably having the same issue that I have, about Dr. Fetus being to slow to catch up with you. You can use The_End254's fix for it, or, if you would like, there is also a small part at the end where you can get under the advancing wall of saws, and can continue jumping there until Dr. Fetus shows up, and then you can pass through to the end part.
And just in case you are wondering, you can do this in the Dark World version of the boss battle, too.