The why's and how's of Harry Osborn's return to the Spiderverse during Brand New Day were never addressed at the onset of that new status quo. This kept Harry's character a bit mysterious as the storylines progressed. Since then, however, bits and pieces of the mechanism behind Harry's return were revealed. Amazing Spider-Man Family #4 addresses the immediate response by Peter upon the news of Harry being alive. His return is further supplemented by Amazing Spider-Man #581-582, which take place well after the onset of Brand New Day. These stories provide some of the details surrounding the cover up of his "death".
In Amazing Spider-Man Family #4, Aunt May shows Peter the newspaper that contains the headline announcing that Harry Osborn never died. Soon after, Harry comes to Peter's house to talk to him in person about this revelation. But Peter does not respond well, greeting his friend angrily as he knows the Osborn's history of mind games and lies. Eventually Peter calms down and lets Harry share some of his story. He tells Peter that the three years he was "dead" are most blur to him and that his father's story that he was on "Oscorp business in Europe" are not true. Harry goes on to say that while he was in Europe, he had another breakdown and that Norman said it was because he was using again. But Harry claims that he doesn't remember much of anything, only the last "few months" of going to therapy has allowed him to find himself again. Peter is still very reluctant to accept Harry, but as he reflects back on their friendship he decides to give Harry a second chance. This sequence of events preceded those of Brand New Day.
Peter accompanies Harry to New Jersey because Harry has some “business with Liz” in Amazing Spider-Man #581. According to Harry, there’s an issue with his life insurance policy and he is going there to help her out. During the car ride to Liz and Normie's home, Harry decides to tell Peter the whole story surrounding his “death”. In short, he says he took the Goblin serum, it was in his system, it brought him back. Peter response is that he had thought the Goblin serum killed him, telling Harry that Spider-Man told him that those were his dying words. Harry says that he said that because he was “high” on Goblin serum. Harry goes on to say that he didn’t pull this off by himself, there was someone else who took care of it. A flashback scene reveals Norman Osborn bribing two medics at a morgue. Norman also had the help of Mysterio who was charged with the task of switching the autopsy reports and getting a genetic duplicate for the coffin. Mysterio reminds Norman that he has to be the one to “sell this”, with graveside visits and references to his departed boy.
Even though Harry doesn’t mention his father’s name explicitly, there's a good chance he's aware of what his father did since they were in contact while he was in Europe. However, it's not clear whether or not Harry knows if Mysterio was involved at all, he does not say his name explicitly either. Harry then states that for the next couple of years Norman placed him in all kinds of clinics, claiming that he needed to detox. They had him convinced that his days as the Goblin were a drug induced hallucination. His memory was jogged when he saw his dad in the Goblin suit (during the New Ways to Die), and that most of his memory came back in pieces. Interestingly, he doesn’t remember everything, including the fact that Peter is Spider-Man. When he did return to the public, he wanted to live a better life and do good for others. That is why he rebuilt Aunt May’s house, the one destroyed by Charlie Weiderman before they moved into Avengers Tower.
In Amazing Spider-Man #582, the second part of this story, we learn that the Promethean trials were set up by Harry as a means to help Mark Raxton, and to help balance the scales in his relationship with Liz. That was the reason for him taking the Prometheus X-90 serum (at the conclusion of New Ways to Die). The serum should purge the Molten Man of his molten material. He also developed the serum on one human volunteer, Charlie Weiderman, and that is how Harry knew to rebuild Peter’s home.
Harry's return adds new wrinkles to the Spider-Man mythos. Certainly Norman was doing his part to cover up Harry's death during that memorable scene at the graveyard during A Death in the Family. However, some of Norman's motives become questionable now, for instance, his return at the conclusion of the Clone Saga. Norman returned from his European exile, to exact revenge upon Peter's offspring to settle the score for what Peter had done to him. Not to mention the numerous other instances of Norman's badgering Peter because Peter had taken his only heir. This can all be rationalized by stating that Norman Osborn is one maniacal being, and he knew how to hurt Peter by talking about Harry. Thus Norman was not lying, just pulling Peter's strings at times to manipulate him further. Another question about this return is that Norman had an excuse for his phoney death, he claimed to be hiding from his enemies. But if Harry doesn't have that excuse, isn't it illegal to fake your death?
Aunt May is the first to inform Peter that Harry is alive, as seen in Amazing Spider-Man Family #4
Peter forgives Harry and their friendship is restored, as seen in Amazing Spider-Man Family #4
Amazing Spider-Man #581
Harry greets Peter and Aunt May after restoring their destroyed home, as seen in Amazing Spider-Man #581
Harry doses Raxton with the Prometheus X-90 cure, as seen in Amazing Spider-Man #582
s seen in Amazing Spider-Man #582