This really isn't the end of Will's problems. Buffet Froid, an analogy to the act of serving yourself, but also referring to the 1979 French film with the same title makes a point to uncover Will Graham's state of mind. Unfortunately, he is left in the dark, and the act of dehumanizing him by hiding the truth becomes apparent.
Well played, Dr. Lecter.
In a session with Hannibal, Will is confronted with the problem of feeling alive or not, and he summarizes it with the word "fading". An apt description, considering how he seems to lose himself in the process of reconstructing cases to the point, where his own identity becomes a question mark.
What does it mean for Will to experience a loss of time, to experience spatial neglect as well as hallucinations and an empathy disorder?
It isn't quite simple as overcoming delusions, as Hannibal suggests. One could clearly see how
Will didn't simply reconstruct the thoughts of a killer, but immersed himself completely in it. And this problem leads to Will's own belief that there must be other reasons, neurological in nature that lead to multiple symptoms separate from his mental health.
Identity
He interferes and actively takes Will's agency away from him, although the hints at Hannibal's own interest in Will's conclusions of each case is constantly heightened.
Notice, how the camera focused on Hannibal's reaction when Will suggested that the killer was sad and lonely and that this murder is not based on being savage.

No treatment can lead to a bleeding in the brain and a permanent brain damage that affects all senses. Memory loss, seizures, fever, disorientation, headache and a potential autoimmune disease are just one part of Will's problems. And Hannibal knew it all along. His manipulation becomes absolute, and Will is ultimately left with the impression that all of his symptoms are cause of a mental illness rather than a physical viral infection. Hiding the truth from him means that Hannibal takes control of Will's identity construction, his search for stability and treatment. His life is now in Lecter's hands.
Parallels

Intentions
Hannibal swears he will "put out the fire", but my impression is that he wants to pour some more oil on it, having a fire that consumes everything in the process.
His intentions are obscure, but also easy to link to his own identity construction. In the end, Will might become what Hannibal wants him to be, and by doing so, he gains power, stability and maybe even a companion. In the end, Georgia sees Hannibal killing the neurologist, but cannot recognize his face. Even Crawford himself remarks on Hannibal's lack of interest in his colleague's death, which Lecter drily summarizes with having grieved his death already and now being interested in the person still alive. Will Graham.