Alexander Conklin was a Special Activities Division Coordinator and Chief of Operations in Europe. He directly oversaw field operations conducted by Treadstone at the time of Jason Bourne's contracting amnesia and disappearing. He serves as the main antagonist of the first film.
In The Bourne Identity, Conklin is first seen sitting at his desk observing a printed surveillance photo of Nykwana Wombosi's yacht when Danny Zorn alerts him of the ambiguous failed mission, to which Conklin appears to prepare to respond appropriately. He's next seen entering into the CIA's facilities in Langley, Virginia when the Treadstone team learns of Bourne's encounter with authorities in Zürich. Upon realizing the scale of the damage inflicted by Bourne, Conklin orders his team to activate all available agents to track Bourne and kill him. While the agents individually trace and engage Bourne, Conklin remains at the Treadstone office working constantly with analysts to figure out what Bourne's intentions and whereabouts are. He's notified by Nicky Parsons when the first Treadstone agent Castel unsuccessfully attempts to take Bourne out at his Parisian home, resulting in Bourne disabling and interrogating him followed by Castel's suicide when Bourne left a window of opportunity.
Conklin and his team continue throughout the movie to trace his whereabouts and cross-referencing any information they receive with Bourne's accomplice Marie Kreutz's history. They manage to track them to a pay phone south of Paris and eventually to Marie's step brother Eamonn's home in the French countryside. It's at his home that Bourne encounters and engages The Professor and first learns of Treadstone. After Eamonn takes Marie along with his family away from Bourne and the danger that surrounds him, Bourne goes through the Professors things and comes across his cell phone. He dials the last called number which puts him through to Nicky who in turn patches him through directly to Conklin in Langley. After a brief conversation with Bourne, Conklin embarassed and frustrated in front of his superior, Ward Abbott, instructs Danny to contact Nicky and tell her to prepare for his arrival in Paris. He has decided to handle the matter personally as Bourne has instructed Conklin to meet him on Pont Neuf later that day. When Conklin arrives at the designated meeting spot, he sets his team in place ready to apprehend Bourne when he arrives. However Bourne has observed the whole thing from a high vantage point and notifies Conklin that he's gone. As he departs he discreetly places a tracking device under the bumper of Conklin's van and follows the van to the Treadstone safe house from which Nicky works.
It is at the safe house that Bourne bypasses the agents guarding the outside and scales the wall to infiltrate the room. He shuts off the power and phone lines as Conklin is working to dispose of the files Bourne may want, Conklin then retrieves Nicky's handgun from her field box to try and stop Bourne. However Bourne tricks him and interrogates him as to who or what Treadstone is. Conklin misunderstanding Bourne grills Bourne in return to find out what exactly happened in the failed assassination of Wombosi. Bourne begins to finally recall the events that had transpired weeks earlier on Wombosi's yacht and proceeds to knock Conklin unconscious after he realized Conklin had notified the agents outside. After dispatching all of the field agents, Bourne departs and Conklin leaves soon after.
In the final scenes of the film, similar shots of Bourne and Conklin are seen as they both limp down a dimly lit side street in Paris combined with shots of the Treadstone operative Manheim fixing a suppressor onto his handgun. As he exits his car, preparing to kill one of them it is revealed that his target is Conklin whom he shoots twice in the chest and a final killshot in the head. It's then revealed that the order came down from Abbott to have Conklin killed and Treadstone is officially disbanded.
Conklin is only mentioned in passing or seen in either flashbacks or when his service jacket is viewed on screen. In The Bourne Supremacy, Conklin is seen several times as Jason has dreams and flashbacks of his first mission in Berlin, Germany when he assassinated Vladimir Neski, Conklin was onsite to oversee that Bourne's training was complete through his accomplishing the mission.
In The Bourne Ultimatum Conklin's service jacket is seen with his ID photo amidst many of the other victims of Treadstones operations.