Originally Posted by
Kingkalamari
The biggest problem with trying to address this is the fact the story is so inconsistent, but here's my head canon at least, trying to make a explanation.
Harry dies, goes to hell, as we see at the start of #74. We see Mephisto scolding him over his sins of the fake parents and the Stacy twins, baiting him to believe he could never be a good person. Harry slowly corrupts and turns into Kindred, and proceeds to start hatching a plan by recruiting the likes of Mysterio.
The Stacy Twins emerge, with a iteration of Mephisto overseeing it, influencing the Harry AI to be extra-deranged (Mephisto can operate and be in multiple places at once).
OMD happens, Mephisto is satisfied, but not satisfied enough. Plucks part of Harry's soul from hell and throws him in the Stacy lab, where he becomes a human again. The "European Estate" of the Osborns is reality warped by Mephisto to cover the tracks, and Norman doesnt think anything of Harry's return. If Mephisto can get Harry to have another snap and go evil again, he's got limitless amounts of suffering to wedge between Peter and MJ. He also has Harry go to Europe for regular "business trips", which are actually just cleaning up after the Osborn twins clones going astray, which he is ashamed of and hides from everyone.
This Harry however, doesn't behave the way Mephisto expected. Instead of being the same old Harry, he instead changes for the better, turning against his father and doubling down as a ally to Peter. It's annoying, but it's not a big deal, since Mephisto as numerous plans.
Peter and MJ get together, and Mephisto launches his big ace in the hole: Kindred. Using the Stacy Twins as vessels and the corrupted soul remaining of Harry in hell, which he puts into the Harry AI in the lab, creating a techno-demon of sorts, Mephisto releases Kindred to break the two up. The opening salvo being during one of Harry's routine checks to the lab, Kindred abducts and jails him, leaving him alive to make sure Harry will be broken and end his good streak.
Jump to the end, and BND Harry sacrificing himself in selflessness against the person he hates most breaks Mephisto's grip on Harry's soul, no longer able to dupe Harry to believe that he deserved to be in hell. Harry's soul reunited is able to be at peace, ending Mephisto's plan.