He had a very strong interest in Jane Doe and has concerns that her tattoos could reveal information that would implicate himself and FBI Assistant Director Bethany Mayfair in a project called Project Daylight.
Involvement with Orion
Carter was the head of Orion, a CIA-sanctioned group for illegal operations that was shut down after the project's existence was compromised by Douglas Winter.
Trying to keep his name out of the involvement with Orion, Carter ordered to shut down the operation. This led to the death of a group of Navy SEALs while they were on a mission in Afghanistan, however, the only survivor was Remi.
Involvement with Daylight
Thomas Carter alongside Bethany Mayfair and Sofia Varma were called to be part of Project Daylight, a secret group project between the White House, CIA and the FBI agencies that gathered and distributed illegal NSA information for the government.
When the project was shut down, Carter, Mayfair and Varma were left alone to defend themselves of what was about to come for them.
Carter's agents followed Jane Doe and took her to a basement where he applied the waterboarding torture method in order to get information about her real identity and her goal inside of the FBI. When he was about to use a drill as another method of torture on Jane, Oscar shot Carter to death.
The circumstances surrounding his death, became a mystery, especially to Bethany Mayfair who asked Edgar Reade to investigate Carter's disappearance. It also caught the attention of Jonas Fischer who opened an inquiry inside of the FBI to find a presumed mole responsible for Carter's death. It was finally stated by Matthew Weitz that Bethany Mayfair was Carter's killer and she was taken under arrest.
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