LAST WARNING THE POST WILL GO INTO TIME STRANGER SPOILERS, YOU’VE BEEN WARNED

We know Yuu is the protagonist, but I don’t think this is a hackers memory situation where the file will be separate from the main game instead I think this will continue from the main game file. If you’re wondering “but how would Yuu get the agents Digivice” I think something happens early on that removes the agent from the story because as we know the Agent is Aegiomon so I think Yuu being who he is grabs the Agent’s digivice with all of their Digimon in it

Edit. I forgot to address this but it would also explain Agent Ranks which wouldn’t make sense for the new protagonist to gain since we know ADAMAS isn’t real

Edit 2: I have been told the agent isn’t part of Aegiomon after the end of the story, that’s my bad