In Amazing Spider-Man #12, Doctor Octopus defeats Spider-Man once again. To make matters worse, he also unmasks him in front of J. Jonah Jameson, Betty Brant, and scores of other onlookers. Luckily for Spider-Man, a bad case of the flu has made him so weak that basically no one, including Doctor Octopus, actually believes that he’s the real Spider-Man. Instead, everyone just assumes that Peter had dressed up as the wall-crawling hero in order to save Betty Brant himself. That wouldn’t be the last time that Doctor Octopus learned Spider-Man’s true identity, however.
In The Amazing Spider-Man #397, Doctor Octopus discovers Spider-Man’s secret identity once again, this time in order to cure him from a fatal virus. Doc’s newly acquired altruism comes from a desire to see his old foe as the happy-go-lucky superhero he used to be, rather than the dour, hyper-violent vigilante he’d turned into (as was common in extreme ’90s comics). Luckily for Spider-Man, Doctor Octopus is almost immediately murdered by Kaine, Spider-Man’s murderous clone brother, before he can put that information to use. By the time he’s eventually resurrected by the ninja cult the Hand in The Amazing Spider-Man #427, he no longer remembers that Spider-Man is Peter Parker.
Of course, Doc Ock learns Spider-Man’s secret identity yet again (along with the entire Marvel Universe) when Peter unmasks himself on live television in Civil War #2. Doc Ock, along with nearly the entire Marvel universe, then forgets that Peter Parker is Spider-Man after the wall-crawling hero makes a deal with Mephisto (basically Marvel’s version of Satan) to make his identity secret once more.