William Bell and Walter Bishop were lab partners at Harvard University. Although it is unknown when Bell specifically began plotting Neogenesis, both he and Walter were consumed with defying nature from a very early date in their partnership. Eventually, the two became aware of the existence of an Alternate Universe and created the drug Cortexiphan. Bell built his Massive Dynamic empire by stealing Alternate Universe technology. He also crafted the ZFT and wrote its manifesto. Bell used Massive Dynamic as a front for ZFT, applying its resources and using it to funnel money to the terrorist organization. Eventually, Bell crossed over to the Alternate Universe and began provoking a war. He supported the Walternate and helped him craft the shapeshifters. Meanwhile, ZFT was laying the groundwork for the coming war in the Prime Universe. William also became aware of The Vacuum. He obtained many copies of the First People book in order to study its origins and function. After his apprentice, David Robert Jones, a former Massive Dynamic employee, escaped prison, Jones began to search for a way to cross over to the Alternate Universe to meet up with Bell. However, Jones was killed by Peter Bishop in the process of crossing over. This seemingly put an end to the Neogenesis plot.
Bell later helped the Fringe Team return back to the Prime Universe after crossing over and sacrificed his life to help them. However, Bell knew this would not be the end. He had given Olivia soul magnets when she crossed universes in 2009. He expected, and rightfully so, that there would come a day when he was brought back to life. However, nothing came of this, as he was purged from Olivia's subconscious soon after.
In the Alternate Timeline, Peter Bishop died as a young boy. Because of this, he was unable to stop David Robert Jones from crossing universes, which in turn ensured the Neogenesis plot would continue. After crossing over, Jones and Bell worked on creating a new breed of shapeshifter. They also worked at creating new species for the new universe and loaded them on the SS Talos, a ship that would be the only surviving object of both universes when the third universe was created. Jones began mining amphilicite, a powerful mineral that would be capable of blasting holes in the very fabric of the universe. Jones tested the substance on the town of Westfield, which was successfully obliterated. Jones later created devices powered by amphilicite and ran several tests with them that resulted in the death of the individuals involved, both themselves and their alternate universe counterparts, regardless of where the counterparts were located.
This was a test to find a frequency that could link both universes. He then gave Colonel Broyles of the Alternate Universe a device to attach to the First People Machine, which would collapse the universes. Broyles turned himself in instead of using the device however. Bell began activating the Cortexiphan children, who had been actively recruited into the ZFT fold by Jones and reciting catchphrases of the organization to Olivia during interrogation. These agents were weakening the fabric of the universes in order for Bell to collapse them. The Fringe Division caught onto the plan and closed The Bridge between universes as a last resort to stop the plan. That did not stop Bell, however, who activated Olivia, the most powerful of the Cortexiphan children. He took the SS Talos into the ocean at a neutral location that would survive the destruction of both universes. Walter took desperate measures- shooting Olivia in the head- to stop the plan once and for all. After William Bell disappeared off of the SS Talos, Walter and Peter were able to remove the bullet from Olivia's head and allow the regenerative properties of Cortexiphan to heal her, bringing her back to life.
After the Observer Invasion, Bell began cooperating with the Observers. He feigned an alliance with Walter and the other members of Fringe Division but sold them out. It is unknown what Bell's objective was with cooperating with Observers and if it had anything to do with reinstating Neogenesis.