The Abu Sayyaf operation ended up not being as quick and easy as everyone had thought it would be. Although no one knew it, NCIS operative Galib was already dead when Gibbs came aboard, and Gibbs was led straight into a trap by Pin Pin Pula, the terrorist who had assumed Galib's identity. An explosion designed to take Gibbs' life took his memory instead, and a series of unbelievable decisions by the higher-ups a few days later took his spirit. By the time it was all over, an angry and defeated Gibbs had 'retired' from NCIS, left Tony in charge, and headed off to Mexico to join another bitter ex-NCIS agent, his old boss, Mike Franks.
For his part, Tony took over the leadership of the team, almost against his will. Any praise or accolades he'd received after the bank situation faded quickly as people closely watched his every move, wondering if he was truly going to be able to "be Gibbs."
A few weeks after Gibbs left – and then came back again to help Ziva out of a situation of her own and then left again – there came a report of a possible connection between the son of a high-ranking officer and a suspected meth lab being run by both Marines and Naval personnel. A task force was put together to find the lab and clear the son's name. Tony was offered the NCIS slot on what was to be a short, but potentially dangerous, undercover mission. He jumped at the chance to get out of the office and away from the unsure looks and doubting comments of his new team.
The mission didn't go quite the way it should have, however, and about two weeks in, Tony found himself black-and-blue and tied to a chair in a warehouse in upstate New York, hoping that someone would think to come looking for him.
But …that's another story …