This is a really legal gray area. You could write the entire story just about the legal case.
The definition of death is medical & biological: end of heartbeat or brain activity: https://en.wikipedia.org/wiki/Legal_death
His form and memories are too imprecise and abstract to argue over.
Argument for citizenship would be the strongest if the transformed body has a heart that beats and brain that generates recognizable electrical signal. It would also help if there is no body (and no biological matter) left over after his transformation.
The argument against him being alive is that he is a fancy robot equipped with advanced chatbot and voice synthesizer. With a few more advances in modern technology, you could create a fairly convincing imitation of a human being. Chatbot and visual recognition system can be trained with things that a specific person is supposed to remember. So if we grant citizenship to your protagonist, should we grant citizenship to those robotic copies as well?
Even if he does have have a brain, the key argument here might be whether each neuron of his old brain was copied or transformed into the new form, and if they function the same way. If yes, his new brain could be viewed as a form of prosthetic (similar to artificial heart), so he is a person. If no, his "brain" is a fancy computer similation, and not a person.
There might be a middle ground actually: he is declared to be a person, but a mentally disabled one, and hence a ward of the state or his parents or family.
The example here is people with brain injuries or dementia - they might have lost good chunk of their memories, skills and personality traits, but they are still the same legal person. But they will never be trusted to make financial decisions, drive cars, use kitchen knives, etc.
PS It might not matter much: he will likely be locked up in a government institution in either case. B/c even if he is a person and a citizen, he is still made out of some unknown matter, which might be radioactive, or can explode when exposed to some specific chemical, or maybe his breath is toxic, or maybe it takes time for the negative effects to build up. And most importanly, maybe his condition is contagious, or he can spread it under the right circumstances.