Seems like yet another reference to Operate Shooting Star's mysterious time travel aspect, possibly even a poke at Clock Man, the time traveling Navi from the future. Not really sure what to make of this one, though it really makes me question the true identity of Clock Man (Clark?)
"A while back I mentioned something about a “program that can control time,” but it seems like they somehow completed a prototype!
Then, Ace comes to me and asks of all things “Clark, if you’d like, would you want that program installed in you?” It seems to be for data collecting, but to get a program like that installed… I get kind of a special feeling. Hmm, but why would Ace choose me?"
Credit: TwilightTO and The Mega Man Network