Captain Windmark is an Observer. In 2036, he fulfilled the role of Occupation Administrator. He was tasked with policing civilians. When asked by Broyles what he did in 2609 to get this kind of detail, Windmark simply responded that he likes "animals." He is cunning and ruthless in the face of adversity.
Captain Windmark is in charge of Occupation Administration in 2036. His jurisdiction appears to be over at least the North American Northeast. Fringe Division, and its head Phillip Broyles answer to Captain Windmark. Windmark attends a nightclub and has a brief encounter with a worker at the club in which he attempts to read his mind. After the encounter, Henrietta Bishop promises to take the man away. Windmark tries to read her mind but is unable to do so. Windmark pays Broyles a visit and warns him that native-on-native crime will not stand. He warns Broyles that he needs to get his Division under control or else the Observers will take it over.
After the original Fringe Division is freed from amber, they begin looking to assemble pieces of a plan that Walter Bishop constructed to defeat the Observers. Walter is kidnapped by Observers and interrogated by Windmark. Windmark tries to read Walter's mind but is unable to make sense of the pieces of Walter's Plan because they had been scrambled by September. Unaware of the true source, Windmark questions Walter about how he learned how to perform such a task. The interrogation gets nowhere and Walter is ultimately freed. Windmark becomes aware of Henrietta's betrayal and begins leading a charge to find and capture the fugitives.
Observers are hot on the trail of the rebels and eventually catch up to them. Captain Windmark takes to the ground and pursues them himself. He corners the team in an abandoned warehouse and engages in a brawl with Henrietta. He pins her up against the wall and begins to read her thoughts before shooting her point blank. He leaves her body in the room and heads back outside, unable to find Peter, Olivia, and Walter. Suddenly, an idea occurs to him. He exploits parental love, knowing that the family would return for Etta's body. The team did return but was able to flee the scene before Windmark arrives. Instead, they left an anti-matter bomb in Etta's hand. Windmark notices it at the last second and is able to teleport out of the warehouse before it is destroyed, leaving Etta and the other Observers behind.
The Observers continue their pursuit of the Fringe Division and follow them to Worcester. A group of Observers enter the Pocket Universe where the Observer Child had been previously stored and confront the team. The fugitives are able to escape. Peter, who had inserted Observer technology into his head, trails behind and engages in a fight with another Observer. He is able to kill the Observer and Windmark secretly looks on.
Peter, driven by grief over the murder of Etta, is determined to get revenge on Windmark. He uses his newfound Observer abilities to run timelines with the intention of catching Windmark off guard and killing him. The Observers discover that the team is using Henrietta's apartment and begin to investigate. It is here that Windmark discovers the timelines and realizes Peter's intention to kill him.
Windmark and Peter engage in a game of cat-and-mouse until a confrontation in an abandoned building. The two fight but both survive the encounter. Peter continues to run timelines and finally creates a scenario that will result in Windmark's death. Peter explains to Olivia that he will know the chain of events is set into motion once Windmark crosses a certain public square. The two look on as Windmark does exactly this. Because of Peter's slow fall from humanity, however, Olivia convinces him it is necessary to take the Observer tech out of his head immediately. He does so and the two resolve to find another way to put an end to Windmark.
Captain Windmark begins to investigate Nina Sharp and her involvement in the Resistance. He and a couple of Observers show up at Nina's office in the Ministry of Science but by the time they arrive, she is long gone. They begin to interrogate workers at the Ministry of Science in order to find out who was aware of the missing technology given to the Resistance to access William Bell's storage facilities. Nina's comm device is tracked and Windmark goes to the Massive Dynamic Black Lab with a group of Observers and Loyalists. Here, he meets up with Nina and begins to question her about the location of the fugitives and Michael. Nina, however, was granted the ability to block her mind from being read by Michael. Windmark is unable to extract any information from her and resolves to torture. Before this is able to happen though, Nina steals a gun from a Loyalist and shoots herself in the head. Windmark and the Observers leave her body in the lab, unable to locate the child or the fugitives.
Windmark goes to 2609 to report the problem at hand—namely Anomaly XB-6783746 is somewhere in 2036 and important to the fugitives. He asks permission to go back in time and prevent the Resistance from ever having the opportunity to implement their plan, but the Commander denies it, citing the 99.999% chance of success in colonization that 2036 prevents. Windmark reveals that destroying the fugitives consumes him.
Windmark continues to feel emotion, specifically hate, due to close proximity with humans. He investigates September's apartment and begins carefully looking at things that could potentially fill him with emotion: a Bible, a snowglobe, and a record player. These things are quite curious to him. He also notices a bomb and is able to teleport out of the apartment before being killed. Michael is finally captured by Loyalists at the train station and the child is brought to Windmark.
Windmark sends Michael to a facility on Liberty Island. After the child is broken out by Olivia, Broyles is pegged as the mole within the Observers ranks. Windmark interrogates him but lets him go, assuming that he will lead the Observers to the Fringe Team. Broyles catches on, however, and leads the Observers on a wild goose chase before being taken into custody. While interrogating Broyles, the Resistance breaks into the facility, killing many Observers and Loyalists, as well as freeing Broyles, but Windmark escapes. He meets the team as they attempt to implement their plan to send Michael to 2167. He engages in a fight with the team and is about to take the boy when Olivia makes use of the remaining Cortexiphan in her system. Windmark turns to face her and witnesses the power in the entire city landscape behind her shut off. A truck is flung at Windmark, sandwiching him in between two vehicles. He attempts to teleport but just misses his opportunity, instantly dying.