Jay Whitaker is the U.S Homeland Security Advisor , second-in-command of the True Believers and traitor in the White House. As such, he was the individual who hacked the White House and inserted the false confession to the Capitol Bombing by Majid Nassar into their computers. He also deleted files connecting certain individuals to the conspiracy and he is responsible for feeding journalist Abe Leonard enough information for the latter to publish a story that discredited Al-Sakar from the Capitol Bombing.
After Hannah Wells obtained pictures and an audio track of him discussing the takeover of the United States from her late partner Jason Atwood, he was promptly arrested at the West Wing.
It is presumed that at some point before the Capitol attack, he allowed the True Believers to access File 12-80C, a simulation on how to destroy the United States Capitol. The simulation would be repeated on the day of the State of the Union and Jay would go on to delete files that pinned certain individuals to the conspiracy, notably the private military Browning Reed and Nestor Lozano. Jay blackmailed Charles Langdon into naming Tom Kirkman the designated survivor and added that he would be killed if he didn't; Jay even told him the color of his tie.
During a makeshift meeting with Vice President Peter MacLeish, who was the incumbent president during Tom Kirkman's time in hospital, Jay told that CTOC could be able to apprehend Nestor Lozano, but MacLeish dismissed that offer and sent command ops troops instead.
Jay began feeding information to Abe Leonard when he sent a link to a website showing Hannah Wells being apprehended by Secret Service. Later that day, he began following Abe, until the latter took a blurred picture of him, which was when he left. On that evening, he left an envelope on Abe's car wipers and called him to meet each other in one hour.
The next day, Jay told Abe that the government was hiding the truth behind the Capitol Bombing and told him to look into Jason Atwood. Later, when asked, Jay provided Hannah with security footage showing "Nestor Lozano"'s journey from the PLC building to the building where he was supposedly killed.
Later that evening, he met up with Abe again and told him to look into Jason's involvement with Majid Nassar and left the scene. After Hannah was kidnapped by Nestor and other conspirators, Jay called him to be informed of progress on kidnapping the FBI agent.
Whitaker received a text from Nestor indicating that Hannah Wells had been taken care of, allowing the conspirators' activities to go uninterrupted. At Patrick Lloyd's house, the two had a brief discussion about their plans for the conspiracy, unknowingly being spied on Jason Atwood.
Chuck found that Hannah had thousands of unread emails, one of which was sent by Jason. After Agent Wells opened his file, she discovered all of the information he had taken before being shot and killed by Nestor Lozano and used this evidence to arrest Whitaker along with Mike Ritter and John Forstell in the West Wing.