In 2003, Maya (Jessica Chastain), a young U.S. Central Intelligence Agency officer, has spent her entire brief career, since being recruited for the agency, focused solely on gathering intelligence related to al-Qaeda leader Osama bin Laden (Ricky Sekhon), following the terrorist organization's September 11 attacks on the United States in 2001. She is reassigned to the U.S. embassy in Pakistan to work with a fellow officer, Dan (Jason Clarke). During the first months of her assignment, Maya often accompanies Dan to a black site for his continuing interrogation of Ammar al-Baluchi (Reda Kateb), a detainee with suspected links to several of the hijackers in the September 11 attacks. Dan subjects the detainee to approved torture interrogation techniques, i.e., stress positions, hooding, subjection to deafening noise, sleep deprivation, waterboarding, and humiliation.
After failing to get al-Baluchi to give up information on an attack in Saudi Arabia, he and Maya eventually trick Ammar into divulging that an old acquaintance, who is using the alias Abu Ahmed al-Kuwaiti, is working as a personal courier for bin Laden. Other detainees corroborate this, with some claiming Abu Ahmed delivers messages between bin Laden and a man known as Abu Faraj al-Libbi.
In 2005, Abu Faraj is apprehended by the CIA and local police in Pakistan. Maya is allowed to interrogate him, but he continues to deny knowing a courier with such a name. Maya interprets this as an attempt by Faraj to conceal the importance of Abu Ahmed.
Maya spends the next five years sifting through masses of data and information, using a variety of technology, hunches, and sharing insights. She concentrates on finding Abu Ahmed, theorizing that he is the best way to find bin Laden. In 2008, she is caught up in the Islamabad Marriott Hotel bombing. Dan, departing on reassignment, warns Maya about a possible change in politics, suggesting that the new administration may prosecute those officers who had been involved in interrogations.
Maya's fellow officer and friend Jessica (Jennifer Ehle) is killed in the 2009 Camp Chapman attack. That same day, a grieving Maya receives an interrogation video of a Jordanian detainee, who claims the man previously identified from a photograph as Abu Ahmed is a man he personally buried in 2001. Several CIA officers – Maya's seniors – conclude the target who could be Abu Ahmed is long dead, and that they have searched a false trail for nine years.
Sometime later, a fellow analyst researching Moroccan intelligence archives comes to Maya and suggests that Abu Ahmed is Ibrahim Sayeed, a suspect who had come to CIA attention shortly after 9/11. Realizing her lead may still be alive, Maya contacts Dan, now a senior officer at the CIA headquarters. She theorizes that the CIA's supposed photograph of Abu Ahmed was actually of his brother, Habib, as he was said to bear a striking resemblance to Ibrahim and was known to have been killed in Afghanistan, and points out that Abu Ahmed's death in 2001 contradicts Ammar's account.
Dan uses CIA funds to purchase a Lamborghini for a Kuwaiti prince in exchange for the telephone number of Sayeed's mother. The CIA traces calls to the mother and quickly identifies one suspicious caller who persistently uses tradecraft to avoid detection. Maya concludes that the caller is Abu Ahmed, and with the support of her supervisors, numerous CIA operatives are deployed to search for and identify the caller. They locate him in his vehicle and eventually track him to a large urban compound in Abbottabad, Pakistan, near the Pakistan Military Academy. As Maya leaves her residence one morning, she is attacked by multiple gunmen, but the bullet-proof glass in her car saves her. Knowing that she has been blacklisted by al-Qaeda and there will be more attempts on her life if she stays, her superiors remove her from the field and send Maya home to Washington, D.C.
The CIA puts the compound under heavy surveillance for several months, using a variety of methods. Although they are confident from circumstantial evidence that bin Laden is there, they cannot prove this photographically. Meanwhile, the President's National Security Advisor tasks the CIA with producing a plan to capture or kill bin Laden if it can be confirmed that he is in the compound. An agency team devises a plan to use two top-secret stealth helicopters (developed at Area 51) flown by the Army's 160th Special Operations Aviation Regiment to secretly enter Pakistan and insert members of DEVGRU and the CIA's SAD/SOG to raid the compound. Before briefing President Barack Obama, the CIA Director holds a meeting of his top officials, who assess only a 60–80% chance that bin Laden, rather than another high-value target, is living in the compound. Maya, also in attendance, states the chances are 100%.
The raid is approved and is executed on May 2, 2011. Although execution is complicated by one of the helicopters' crashing, the SEALs gain entry and kill a number of people within the compound, among them a man on the compound's top floor who is revealed to be bin Laden. They bring bin Laden's body back to a U.S. base in Jalalabad, Afghanistan, where Maya visually confirms the identity of the corpse. Maya is last seen boarding a military transport to return to the U.S. and sitting in its vast interior as its only passenger. The pilot asks her where she wants to go, but she does not reply.
As the plane's hangar door closes, Maya begins to cry softly.

Question: What clue directs Maya to believe Ahmed is still alive?
Answer: Morrocan intelligence that identifies Ahmed as Sayeed
Alternative answer: photograph