Don't Count Bonnie Out

The reason Freddy was fatherly to Gregory throughout the game was because he didn't get hacked by Afton in the start of the game (when threat was detected and he collapsed, thus leading him to wake up in safe mode safe from the hack). The other animatronics were hacked by Afton because they were connected to the main network, as seen when Freddy tries to contact the main office for them to get Gregory and he says "connection error".

But what if Bonnie was still around at the Pizzaplex? What if you were a programmer that worked the night shift and you were tasked with reprogramming Bonnie after his chip was reset by maintenance? He wouldn't have been connected to the main network either, and thus he would be able to help and guide you to safety as well.

Maybe you'd be able to reunite him with his long-lost buddy...and maybe you could use your programming skills to undo the damage Afton did to the other three animatronics.

Maybe...this story would have a different ending.