Well, in the panel where the townfolks found Eggman you can see some small red cubes over his head, the same cubes Infinite spawns when using his powers.
My theory is Eggman got accidentally brainwashed by the Phantom Ruby (at the end of Sonic Forces) and somebody else is trying to take his place, that somebody might be Neo Metal Sonic, Eggman Nega or Infinite himself.
Heavy spoilers:
That's why whoever is talking to Orbot and Cubot got mad that Sonic and the Chaotix showed up where Mr. Tinker was, because that person was expecting Shadow to kill Eggman for him.
Well, in the panel where the townfolks found Eggman you can see some small red cubes over his head,
