A civilian is driving down a road while speaking on his cell phone to someone and discussing his destination when suddenly he is shot dead, just as his GPS tells him "you have arrived at your final destination".
Gibbs discovers that the dead man has been using one of his undercover identities from years ago, when he worked under the cover name of Leland Robert Spears.
Abby finds a tracking GPS planted under the hood of the man's car, a GPS tracker not available to the general public.
After pulling the data from the GPS tracker, Abby tells Gibbs that the man had traveled to a remote location where he had stayed for 56 minutes. Gibbs has her pull up the destination on satellite imagery where they discover a cabin. Gibbs sends McGee and Bishop to check it out.
Just as they arrive at the cabin, the place explodes.
Gibbs and Tom Morrow (Homeland Senior Division Chief) discuss old cases in which Gibbs used a covert identify as part of his undercover work. Morrow tells Gibbs about Michelle Stark, also known as "The Architect" -- so named because she built untraceable identities for the CIA. She was with the firm for 30 years.
Bishop and Gibbs interview Stark who tells them that when covert i.d.s were no longer needed they were removed from every record, except the CIA's classified secure network.
McGee tells Tony he broke into a partition on Spears' hard drive and found that he was gathering intel on a semi-conductor called Gallium Nitride (GaN) which has many military applications and is highly prized and wanted by worldwide military organizations.
Gibb's cover as Spears 20 years ago was a computer technician.
Abby and McGee discover that Spears used Gibbs' undercover i.d. to pose as a computer technician to work at a company called Longview Technics, which is an advanced research company that specializes in Gallium Nitride.
Gibbs poses as Spears and enters the company's building in order to access their network files.
McGee examines the data Gibbs obtains and discovers that Spears had been sending documents via FTP to an alternate location.
After tracing the FTP site location, the team storm the place only to find a dead man who had been living under the name of Edgar Braun, which was an undercover alias for Mike Franks.
Gibbs notices that Spears had all kinds of magazines and books about tattoos yet didn't have one himself. Gibbs tells McGee to find out what he can about Miranda Flemming - the undercover name given to Jenny Shepard who had been working with Gibbs and Franks years ago.
Gibbs goes down to see Speeas' body, this time with a backlight under which he is able to ascertain that the man had a Serbian tattoo which says "Freedom or Death".
While Gibbs and Morrow are interviewing Michelle Stark, McGee tells Gibbs that they've found out that Miranda Flemming's identity is still in use and that she is scheduled to catch a flight to Buenos Aires the next day. The picture associated with Flemming is Michelle Stark.
Stark explains to Gibbs and Morrow that she betrayed the agency because she had been forcibly retired. She says an attaché from the Serbian embassy had approached her looking for backstopped i.d.s. She says that they were going to use the i.d.s to find out more information about Gallium Nitride.
Gibbs has her contact her Serbian handler to tell her that Edgar Braun didn't die, but that he's on life support at Washington General Hospital and is expected to live.
McGee poses as Braun, while the rest of the team poses as medical staff.
A fire alarm goes off. A man dresses as an orderly enters McGee's room and pulls out a syringe full of potassium chloride - which would have induced a heart attack. Bishop and McGee pull their guns. The man is captured and taken in for questioning.
The man admits to all of his crimes, but claims diplomatic immunity.
Gibbs tells Morrow that there is no record of the man being registered as a diplomat, so he has no diplomatic immunity.