William Afton, though perhaps arrogant, was not a stupid man. He knew that the forces he was working with were incredibly dangerous, and that a single slip up could spell disaster. With this in mind, he needed a way to ensure that, in the event that he was captured, killed, or otherwise compromised in the course of his work, his plans would not be stopped.
In the event of his disappearance, William told his son, Michael, to locate a box hidden in his office. The contents of this box included a detailed set of written instructions, hundreds of dollars in cash, an unmarked floppy disk, and several identification and clearance documents pertaining to Afton Robotics. The instructions directed Michael to do the following:
Drive out west to Arizona, near Phoenix, where Afton Robotics was headquartered, and find a hotel to stay in for a few nights. The included cash should've been enough to provide for any travel expenses. While there, he was to work at Afton Robotics as a technician, specifically assigned to the CRMN project. All Michael would have to do is show the included paperwork, and it would be taken care of. Once he gained access to the CRMN testing facility, he was to insert the floppy disk into his handheld assistant, and follow the directions to execute the program. From here, Circus Baby would direct Michael on what to do, and that was the extent of the instructions left for him by William.
Of course, Michael was only given enough information for him to set up Circus Baby, and nothing more. The true scope of William's plot was completely beyond him.
The floppy disk contained a program known as "ringleader.exe," which would override any preexisting directive in the Funtime animatronics, focusing them solely on Afton's "Ringleader Contingency". The contingency plan itself was a multi-step plan geared towards continuing Afton's goals in the event that he became incapacitated.
The primary directive was to get the Funtime animatronics out of the facility and onto the surface. Once on the surface, they could get to work rescuing William from whatever predicament he may have found himself in. They would know where to look, and what to do if they found him. Everything had been programmed in by Afton himself as a part of his elaborate contingency measure.
The secondary directive was to gather all files and documents pertaining to the CRMN project, store them locally onto the Funtime animatronics themselves, and then delete them from all company records. The goal was to leave no possible trace of what Afton was doing with the CRMN project. Once the files had been copied and subsequently deleted, the final step was to destroy the CRMN testing facility entirely, through the use of electrical fires and canisters of flammable gas.
The final directive was to eliminate Michael himself. With the Funtime animatronics out on the surface and under William's control, there would no longer be any need for Michael. Thus, he should be disposed of in order to tie up any possible loose ends.
The contingency, in action, worked almost flawlessly. Michael did everything he was told to, successfully executing the ringleader.exe program. From there, Michael was able to retrieve and upload all CRMN related files onto Circus Baby, deleting them from all Afton Robotics official records afterwards, fulfilling the secondary directive. Soon after, the Funtime animatronics conglomerated into a single entity, tricking Michael into entering the Scooping Room, where he was promptly disemboweled by the heavy machinery, fulfilling the tertiary directive. Finally, using Michael's body as a disguise, the amalgamated Funtime animatronics were able to rig the remote detonation of the CRMN testing facility, which ended up causing a major cave-in event. Amidst the ensuing chaos within the greater Afton Robotics building, the Funtime amalgamation, along with the corpse of Michael Afton, were able to slip out unnoticed, fulfilling the primary directive. In the aftermath of the event, the explosion was attributed to faulty wiring, and the cave-in made exploration of the CRMN facility highly impractical, ensuring that nobody would ever discover the truth behind the project. Michael Afton had been presumed dead, as he was last seen entering the CRMN facility before its destruction, leaving no question about his whereabouts, and discrediting any potential future sightings.
Having hitchhiked back to Hurricane, the Funtime amalgamation abandoned Michael's rapidly decomposing corpse to continue trying to find William. Michael's body, however, was never recovered by authorities, as exposure to remnant had caused him to be reanimated. At the completion of Afton's contingency plan, the Funtime animatronics had merged into a single entity and been released on the surface, Michael Afton had been killed and resurrected, and the public at large was none the wiser.