The first time a Beacon appeared was after an explosion at Quantico in 1987. Colonel Henry Jacobson was the head of the investigation of that occurrence. It was only able to be studied for about 48 hours before it exploded down into the ground. Later, one came up through a gas line at a construction site, where it knocked over a crane bearing the Massive Dynamic logo.
It was hidden from John Mosley, also known as The Rogue, who was intent on acquiring it. September, who as an Observer was unable to get involved, tasked Walter with hiding the beacon until it disappeared so that Mosley could not get his hands on it. Walter took it to the grave of a relative. Mosley abducted Peter and began to interrogate him. He hooked Peter up to a mysterious machine that would enable him to read Peter's thoughts. Through a series of questions, Mosley was able to predict where Walter hid the beacon. The beacon burrowed its way back into the ground before it could be taken by Mosley. ("The Arrival")
The Beacon made a second appearance in the entirely fictional story made up by Walter and told to Olivia's niece Ella Blake. In the story, the Beacon was invented by Dr Walter Bishop, tinkerer, and it seemed to be able to track down individual people, as it arrived at Peter Bishop's safehouse seconds before it was invaded by a group of Watchers seeking Peter's special Glass Heart. ("Northwest Passage")
While investigating September's apartment, Peter discovered a device that led him to Foxboro. A beacon suddenly emerged from the ground and Peter took it back to his house. He spent much time trying to figure out its secrets before it unexpectedly activated. A bright beam of light was emitted from it. Peter followed the light through theceiling and hurried to the second floor, where he found September standing in the glow. September explained that he had been locked out of the universe by the other Observers and that Peter's activating the beacon allowed him to find his way back. He also revealed that Peter was home, albeit in a timeline where he had been erased. Despite this, he was in the right universe. As Peter hurried out of the house to find Olivia, the beacon once again exploded through the ground and disappeared. ("A Short Story About Love")
Sometime prior to 2015, William Bell found two beacons and put them in his safe along with his most prized possessions. The beacons were an integral piece of Walter's Plan to destroy the Observers. In the year 2036, Walter, Peter, Olivia, and Astrid went to Bell's safe to retrieve them. According to Walter in his videos made pre-2015, the beacons are used by Observers to locate points in space and time. The Resistance would use the beacons to locate 2167.
One beacon would be sent through the portal to seemingly act as an anchor, while the other beacon would stay behind in 2036. Michael would be accompanied by Walter to meet with the scientists that created the Observers and prevent them from ever creating the emotionless genetically enhanced humans that would invade in 2015, resetting time. The plan succeeded and the timeline was reset.