Jack is back! Jack is back! Sorry, got a little excited there.
We open with a man being abducted from his car by a team hooded men in two vans. They tell him only that they need him to help them with a problem.
Cut to Jack being questioned by a Senate committee about some of his past interrogation techniques with the now-defunct CTU. Jack admits to having used torture to prevent terrorist activity, and is perfectly willing to be judged for his actions. At this point the proceedings are interrupted by two FBI agents with a subpoena for Jack. The agents (Walker and Taylor) leave with Jack without giving a reason. Jack is told by the senator he must return the following morning at the same time - just 24 hours later.
Walker calls into the office and is told by Janis (Janeane Garofalo) that the man from the first scene (Latham) designed the firewall for Homeland Security. Still at the FBI office we're shown a briefing by agent Larry Moss (apparently running the show) who tells the room they've been following a series of tech break-ins and believe Latham was abducted in order to help the criminals get by Homeland's firewall, Classified Infrastructure Port.
Cut to the bad guys who appear to have roughed-up Latham and convinced him to construct a device to hack the CIP, in this case an air traffic control center which controls part of the Northeastern United States. We see real air traffic controllers talking with a soon-to-take-off flight from D.C to New York.
Walker reveals to Jack (who expects to be indicted after the hearings) that he is there because they have photographic evidence that Tony Almeida (gasp!) is one of the people behind the break-ins and abduction related to CIP, which controls the country's major infrastructures. With Jack not believing that Tony is alive, Walker tells him she's had Tony's coffin exhumed and that a different person had been buried there.
Back at the bad guy den, Tony is very clearly running the show. They are having trouble with Latham's device, and Tony threatens the bloodied man with death if he doesn't fix it quickly.
Despite conflicting popular opinion, President Taylor is preparing for military action against General Juma who has killed hundreds of thousands in Sangala. Her husband Henry is being tasked with handling a pesky reporter, who is working on a story that is against sending troops to Sangala. We hear that the president's son is dead and that Henry may not be handling it well. President Taylor begins to address the joint chiefs.
Latham adjusts the device and it allows Tony's crew to test-break into the air traffic control system. Jack doesn't seem to buy that Tony could be behind a criminal operation, but agrees to look at the material the FBI has on him. Moss and Agent Sean Hillinger have discovered Tony's first crack at hacking the air traffic controls.
Sean is tasked with helping Jack look into the FBI's investigation of Tony.
President Taylor is told the initial invasion of Sangala should not be an issue, and her green light is only awaiting a post-invasion report by the Secretary of State, who does not agree with taking action. She is called out of the meeting and told the FAA has reported a breach, and that the current plan is to quietly decrease air traffic while the investigations continues so as not to create national panic.
Henry Taylor meets with the reporter, initially offering an exclusive for leeway with the story. Henry speaks on the phone with an investigator who is looking into his son Roger's "alleged suicide." Henry is told that Roger's girlfriend had $400,000 sent to an offshore account a few days after Roger's death.
While looking through Tony's files Jack spots the name Gabriel Schecter, a man both he and Tony knew in their CTU days. Jack believes Schecter may be responsible for helping Tony with his initial break-ins. Walker gets Moss to agree to let her take Jack to meet with Schecter, thinking merely Jack's presence will cause the suspect to open up.
On the way Jack tells Walker that Schecter had once been a legitimate tech contractor who went dirty and began selling to foreign governments. Jack and Tony had used Schecter for intelligence, a relationship of which CTU had not been aware. Jack believes Tony is alive but is not convinced he is a criminal.
After giving President Taylor his post-invasion report, the Secretary of State agrees to keep his objections to himself. Kanin tells the president that Henry has gotten the reporter to push back his broadcast for 24 hours.
After being told by Walker that she will shut him down if he lays a hand on Schecter, the two enter his residence. A brash Schecter denies having spoken with Tony and eventually asks for a lawyer. Walker takes Schecter's bodyguard to the ground when he tries to grab her and force her to leave, then gives Jack the go-ahead to do whatever it takes to get info from Schecter. Just as Jack has a ballpoint pen inches from his eye, Schecter agrees to talk, getting out only "The last time I saw Almeida-" before a sniper shoots both him and the bodyguard.
Jack answers Schecter's phone. Tony is on the other end, telling Jack to stay away and that "there's nothing you or the FBI can do about this," before hanging up.
In the process of instructing the pilots to their landing at JFK, the air traffic control loses contact with the plane. Cut to Tony who has taken over the conversation with the pilots, posing as air traffic. He tells one of his henchmen to "get ready to make the course change." Said henchman seems surprised that they're "taking this all the way," to which Tony replies "you just need to do exactly what I tell you to do" as the episode ends.