Well one possibility could be based on
what one of the moderators over at the Spider-Man Crawlspace came up with, who was also one of the very first people to correctly guess that the Superior Spider-Man would be Doc Ock. Basically, when Peter and Doc Ock's minds were momentarily linked via the gold octobot, which is what allowed Peter to make Doc Ock experience all of his memories as if Doc Ock lived them, it also allowed Peter, instead of dying, to be uploaded back into his body. However, because his body had already deteriorated prior to his "death," only the patterns of the right hemisphere of Peter's brain were uploaded. Some of the clues for this can be:
*Peter mentions in ASM #700 that he lost vision in
his right eye. The left hemisphere of the brain is what controls the right-half of the human body.
*All the images he's projected to Doc Ock prior to his death were emotional in nature, as the right hemisphere of the brain that is associated with emotions. Notice also that, whenever Peter is rummaging around in Doc Ock's memories, it's always tied to whatever emotions Doc Ock is currently feeling at the present time.
*SpOck displays far more traits associated with the left hemisphere, such as scientific reasoning and logic, whereas Ghost Peter displays traits that are more associated with the right brain, such as emotions and holistic thinking.
*Ghost Peter is only able to prevent SpOck from killing Boomerang and Cardiac whenever SpOck tried to use
his left hand. The gun that SpOck used to kill Massacre was in
his right hand.
*When Ghost Peter tried to regain control of his body and write a message in Superior Spider-Man #7, he kept saying "c'mon right hand" but the art clearly showed he was actually using
his left hand. Furthermore, when it comes out as nothing but meaningless scribbles, Peter laments that he doesn't have access to the language centers of his own brain. Language skills reside in the left hemisphere of the brain.
*In the preview for Superior Spider-Man #9, we see Peter surrounded by iconic landmarks such as Midtown High and the Daily Bugle, but the letters on the building are all scrambled. Again, suggesting an inability to access the left hemisphere, again the part of the brain associated with language, but no problem accessing the right hemisphere, which is associated with spatial awareness.
Thus the theory goes that Doc Ock may purge Ghost Peter by shutting down the right hemisphere of the brain, essentially giving himself the equivalent of a hemispherectomy. And, just like in those operations, the brain would be able to compensate for whichever half was lost due to plasticity, but there would also be some side-effects such as minor paralysis in the left side and vision impairment.
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