It's been roughly a year now, since The Other showed up and did... some stuff to Peter Parker. But it's just now that I'm actually figuring out the answer to something I've been pondering since then.
Pretty much since that storyline ended, I've been wondering "What was up with Peter's mysterious sickness?" You know, the one that nobody - not Reed Richards, Stark, Pym, T'Challa, or Dr. Strange - could fix? It was a important part of the early issues, and then when Morlun showed up, it pretty much got thrown out the window and never addressed again. I guess eyeball-eating was more important.
I believe it was the recent What If? that Peter David wrote about The Other, that finally clued me in, when Uatu talks about how Peter was suffering from radiation poisoning (or something to that effect). Suddenly it made a lot more sense why they'd been so intent on finding the Hulk. Because not many people know more about radiation than Bruce Banner. Maybe they mentioned that in the story and I missed it, or maybe they never explicitly said it, either way, things started to come together.
The radiation is leftover from his first fight with Morlun, when he won by injecting himself with radioactive liquid, thus blocking Morlun from draining his life force (hey, don't blame me for how weird it sounds - it's JMS' story). Peter did a pretty good job, using enough to be effective, but not enough to kill himself. Unfortunately, when all is said and done, he still pumped radioactive liquid directly into his bloodstream, and you'd have to expect that sooner or later, he'd pay for that.
So that explains his odd malady. Of course, it still doesn't explain how Morlun - last seen decomposing in the nuclear facility - showed up again, but what do you want from me? I'm a blogger, not a miracle worker.