Question: Is it alright for my Protagonist to disappear for a while in the story, leaving a lot of room for the MC to develop and grow? However, this does not mean that the Protagonist has given up on his goal which is death. He still works in the shadows, trying to achieve his goal while the MC gets battered with the ever increasing conflict in the story. The protagonist will eventually reunite with the MC in the Climax of the story. So is this alright? I'm worried about having the reader mistake the MC for the Protagonist and make the story seem like a haphazard string of events, with no story goal.
On the surface, the only challenge I see is that you don't want your protagonist to show up in the final act as a kind of deus ex machina
. In other words, you don't want your main character to be put into a tough situation only to be rescued by the protagonist--which would make the main character's challenge a fake.
In addition to being the primary point-of-view character, a main character should be someone with an inner struggle. How he resolves that inner struggle at the climax should determine the story's outcome. In other words, the main character's choice matters.
For example, in Harry Potter and the Prisoner of Azkaban
, Sirius Black is the protagonist who breaks out of jail on a mission to kill Peter Pettigrew as revenge for Peter's betrayal of Harry's parents. Without Harry's participation, that story looks destined to be a tragedy. Sirius would have killed Peter and then had his soul extracted by the Dementors as punishment for murder as well as escaping prison.
Harry, however, intervenes in the story, resolving his issues over betrayal in his usual way (deciding to risk all to protect people). Consequently, he saves the lives of both Peter and Sirius (though they remain fugitives). He also ensures that at least some people know the truth about which one is the real villain.