Time-travel fix it this and that, what if they time travel and make MORE MESS of everything, making us think the messed-up original finale was much better and beautiful.
Will Graham time travels to the start of season 1 and thought that maybe, JUST MAYBE, Hannibal will not make him undergo such hardships, resulting in the death of Beverly Katz and his dear pseudo-daughter Abigail. So he healed his early-stage encephalitis and showed off his murderous potential.
Well, that made Hannibal think the new killer is an attention-seeking wannabe so he tracked Will down and killed him.
Will woke up again at the start of the season, was angry, made another murder tableau and that resulted in a bloody fight between the Cheesecake killer and Copycat Killer. Did not end well. They both died.
After 5 iterations of fighting, all becoming blood baths, one of them gaining too much international attention that they closed off the state, Will Graham was reasonably mad that the reason why Hannibal loved him was because the doctor CREATED HIM. He was groomed. He was manipulated into his becoming. Curing Will's encephalitis is the start of his independence and non-involvement to Dr. Lecter, and upon becoming his TRUE equal, he became a threat.
Will Graham decided to enter Gareth Jacob Hobbs' case, saved Abigail from his father, pointed Dr. Lecter as the man on the phone, and lived happily ever after in Wolftrap Virginia.
In this iteration, however, Hannibal got his attention for being a cold and ruthless detective. He will come to him.