History of The Plan
The plan to defeat the invaders was devised by Walter and September. The plan was to send Michael, an empathic Observer child, to the moment in time where scientists first thought it would be a good idea to erase human emotion for rational thought. Michael would be living proof that they did not need to take an action as extreme as erasing emotion - they could have both. This would prevent the creation of emotionless Observers, who would in turn never invade in 2015. Scientists would hopefully create Observers in Michael's image. September, who used his abilities as an Observer, scrambled the plan in Walter's head so that it could not be extracted by Observers antagonistic to the group.
The Transilience Thought Unifier Model-11 was to be used to descramble the pieces in Walter's head and shed light onto how they all fit together. Unfortunately, in 2036, Walter was tortured by Captain Windmark. The trauma was so severe that even the Thought Unifier was unable to repair the damage. A man named Donald assisted with Walter in the plan. Donald is later revealed to be September. He was banished by the other Observers for sympathising with Walter. They subsequently removed the technology from him and performed a biological conversion, making him human.
Pieces of The Plan
Walter created a device that would get rid of the Observers. Henrietta and Simon showed Walter the device via hologram after removing him from Amber. He explained that he could build it, but it would take time. The device, which consisted of other pieces, would allow for time travel to the year 2167.
Walter left a detailed set of Betamax Video Tapes, detailing where all of the pieces of The Plan could be found. This was meant to act as a failsafe should something happen to Walter. It was meant to allow people from the future to execute the plan, regardless of whether or not Walter was still alive. The videotapes were ambered in the Harvard Lab but stored out of sequence. The Fringe Division began to watch the tapes after Walter's memories were damaged by Windmark. However, because of their old age and the ambering process, the tapes were extremely damaged, making it difficult, but not impossible, to decipher their messages.
Transilience Thought Unifier Model-11
Transilience Thought Unifier Model-11 was stored at Grand Central Station. It was to be used to reorganize the pieces of the plan in Walter's brain so that their intent could be fully understood. Walter sent Olivia to retrieve the Thought Unifier in 2015. He also gave her an ambering device should she be compromised. She was able to retrieve that device but was unable to return to Boston in time. She ambered herself and the Thought Unifier on her way home. Both Olivia and the Thought Unifier were recovered in 2036 by Peter, Walter, Astrid, and Henrietta. Even the Thought Unifier, however, was unable to decipher Walter's memories after the trauma he endured at the hands of Captain Windmark.
The crystallized quartz was discovered in the mines a rural Pennsylvania dwelling. According to Walter's tapes, they will supply a powerful energy source essential to executing the plan. Walter estimated about forty pounds were needed for the plan. Donald was dragged away by Observers years before at this very site. The quartz would act as an energy source to power the device. While it would not start the device, it would continue to power it once it had been activated.
An equation, recognized by Walter as being physics, was hidden at the Newark-Penn terminal in a vent. The equation was written in Walter's handwriting on a large piece of parchment, but Walter was unable to understand it. He believed it was dictated to him, perhaps by September. The team met with Broyles, but the reunion was cut short after they were discovered by Observers. Broyles took the equation to keep it safe.
The Observer Child discovered by the Fringe Division during the beginning of their Pattern investigations was rediscovered by Walter. Walter and Donald created a Pocket Universe to store the child in until he was needed. However, at an unknown time, Donald moved the boy to a family in the woods. He left behind a radio that would transmit the boy's location, named Michael, to anyone seeking out pieces of the plan in the Pocket Universe. The Fringe team recovered Michael from his family and brought him back to their lab at Harvard. Michael was needed as one of the most integral parts of the plan. He would be sent forward in time to 2167 to the moment where the Observers were first created. He would be living proof that emotions did not need to be sacrificed for higher thought. The scientists would then make a different choice and not create emotionless Observers, but hopefully, empathic Observers in Michael's image.
The Plan required two Beacons, which were stored in William Bell's storage facilities. To gain access to the facility, Bell's handprint was required. Walter chopped off the hand after being removed from amber. The beacons were recovered by the Fringe Team and stored in the Harvard lab. The beacons would act like a tether, one in 2036 and the other in 2167 so that time travel would be possible.
An industrial-size electromagnet was required from a scrapyard in Fitchburg. Olivia was sent to retrieve the magnet, where a woman named Simone had been appointed to safeguard it. Simone received this mission from her mother, who had met with an "older man" many years before. The magnet was left on a truck for twenty-one years, always at the ready for the day when it would be needed. Olivia drove the truck back to a storage facility held by the resistance in Boston.
An initiating reactor was necessary to generate the wormhole that would allow time travel. While the quartz would sustain the reaction, the reactor was needed to set the entire plan into motion. September went to December to obtain the reactor from 2609. However, December was killed by Loyalists before he could turn the reactor over. Instead, the Resistance turned to Plan B: using an Observer shipping lane to generate the power needed.
Someone was needed to escort the boy to 2167 and explain his significance. Walter volunteered because he felt it was his chance to redeem himself for breaking the universe in 1985. Walter would sacrifice himself and be erased in 2015 when the Observers invaded. Walter needed to live his 2036 future in order to fulfil his plan that would prevent evil Observers from being created, which would in turn reset time when these Observers did not invade (It's possible that scientists still observed the past, accounting for Peter's existence in the Final Timeline. The plan was never to prevent Observers from being created, but to make them empathic and not invade.) However, if the entire timeline was reset, Walter would never live his 2036 future and send Michael to 2167. In the Final Timeline, the scientists would create Observers all over again and create a neverending time loop. To rectify this paradox, nature would erase Walter from the final timeline at the moment of the reset (2015). This enabled his 2036 version to still exist in 2167, as it would not be replaced by his current, Invasion-less self, setting time back on balance and preventing a future time loop.