Kendall as the head of the FBI tribunal brought in from Washington DC interrogated Sydney Bristow after she was arrested following evidence linking her to a prophecy by 15th century prophet Milo Rambaldi which suggests she could be a national security risk to the United States. Kendall questions her on every aspect of her life, until she is broken out of FBI custody (Q&A).
Kendall then reappeared in the second episode of season two, assuming command of a joint FBI/CIA taskforce working to bring down the criminal organization the Alliance and primarily, their SD-6 cell, though his reappearance coincided specifically with the surrender of Irina Derevko to the CIA (2.2 Trust Me).
Nine months after Sydney's apparent death, she contacted Kendall after escaping from The Covenant. She told him what she saw at her funeral, how her death was faked, the torture she was put through at the hands of The Covenant, and how she became Julia Thorne. Kendall convinces her to continue as Julia Thorne in order to gather info, after telling her that everyone believed she was dead and had started to move on.
Julia/Syd in search of the Cube discovered Lazarey, an expert close to uncovering the artifact. The Covenant wanted Julia/Syd to kill Lazarey once he found the Cube, but Kendall orders her to cut a deal with him and work together, resulting in Syd faking his death at her hands.
After finding the Cube, Sydney was supposed to hand it over to Kendall. But in place of the Cube he receives a video message from Syd telling of her plan to hide the Cube and have her memories removed so that no one will ever be able to find it. She asks him never to tell her what she's been through (Full Disclosure).
Kendall has Sydney tranquilized at her home and taken aboard a jet in order to have a private meeting with her. He reveals he's not FBI but Special Research. He also says that he knows what happened during Syd's missing two years but kept silent because she asked him to. Kendall then proceeds to inform her of what happened during those years.
Kendall says he respected her wishes, but when she went for the cube four months after reappearing in Hong Kong he thought it was best to tell her (Full Disclosure).