Season 2

After Trout is left a cryptic message about the death of Colonel Earl Swanson the three members of the SOF team (Matt, Marge & Benny Ray) are asked to conduct an unofficial investigation into his murder. The team then find themselves put in danger by one of Trout's former operatives, someone that they suspect may have gone rogue.

Heather Young [ Claire ], Steven McCarthy [ Motel Clerk ], Avery Glymph [ Valet ], Philip Pretten [ Warden ] Miguel Santiago, the no: 2 in a big arms dealing organization and now in prison, agrees to sell out his boss and testify against him. His boss puts a $5 million dollar bounty on his head. There are rumors that the US Marshall service may be involved in trying to kill Santiago and collect this bounty so Trout wants his team to keep Miguel alive for the trial.

In Rumansk a struggle for control of the country leads to the assassination of the defense minister and the kidnapping of his mistress. Roxanne Mitchell is more than just his mistress though; she is also an undercover CIA agent who knows Trout's identity. Matt has to lead the team into a foreign country to rescue her, or kill her.

The team's best friend in the Senate, Senator Stanford Parks, comes to Xavier and tells him that his daughter has gone missing. She was last seen in leaving a club in the company of Alex Vargas, the son of a big time drug lord in Columbia and someone known to take his ladies back home with him. He wants the team to head into Colombia, find his daughter and bring her back. Meanwhile his daughter has seen something she shouldn't have and her life is in danger.

Margo goes on a solo mission to Berlin, delivering money to an agent in exchange for a list of names that the American Government may be interested in. Her contact is found dead and she is soon in the hands of the German police, being questioned for murder. The rest of the team head straight for Berlin to help her and get her out if need be.

A trade involving prisoners, between Libya and America, is arranged to take place in Iceland. On route to Reykjavik the three Libyan prisoners manage to escape their bonds and force the plane to crash land in Maine. Trout wants the team to not only find the Libyans, in the mountains of Maine, but to do so within a couple of hours and to bring them back alive so that the trade can still go ahead.

What seems, at first, like a simple find and extract mission is hampered by two facts. The first is that the man they have to find and rescue is the nephew of Saddam Hussain and the second is that he is being held by the Iraqi's in their UN Mission in New York. Nick is also bothered about returning to New York for some reason or other, but he refuses to tell the team why.

The US Government thinks that they have finally discovered the identity of the notorious terrorist Gabriel. Matt and his team head out to Switzerland and start a surveillance operation on Johann Miller, the suspect. Their mission orders are not only to determine if he is Gabriel but also what he is up to if he is.

A couple are killed while on the way to the airport. Trout's people, who were attempting to uncover their connections with terrorists and arms dealers, were tailing them. Trout gets Margo and Matt to go undercover as the Jensons to find out more, and more importantly who hired them.

Katrina Herrera (see Déjà Vu & Apres Vu) is released from prison, her case dropped due to lack of evidence. She wants revenge on the SOF team for what they did to her and her father. The first member of the team she goes after is Benny and she kidnaps his son to draw him into a trap. Shepherd argues that they should be careful and not rush into things but Benny lets his emotions get the better of him and wants to do things himself.

Algerian terrorists are blowing up CIA facilities in France using explosives not available for many years. A trip to France brings back pieces of Margo's past as a CIA agent. Including an arms dealer lover, recently released from prison after being caught by the CIA and Margo eight years earlier. To find him, and reconnect with him, Margo has to go back undercover as his lover and a fellow arms dealer, just like she did before.

Margo and Matt visit Margo's brother, John, at a religious conference he is attending in Los Angeles. While they are there Matt spots some unusual jobs being completed by the security personnel. As he tells Margo what he has seen his fears are confirmed by the sudden announcement that the conference has been taken over by terrorists. In an unusual turn of events the leader of the terrorists demands that the American government deliver 20 million tons of wheat to the starving nations of the Third World. This gets not only the majority of the hostages on their side, for their aims if not their methods, but also a lot of the press outside. Matt doesn't trust them though and wonders what they are really after.

A mission at the Transpacific Oil Refinery in Detroit, looking for proof of their illegal activities, goes badly wrong. Benny Ray and Margo are badly injured and end up in a local hospital. Before long the FBI and the NSC are there, investigating two people they think are foreign spies trying to gain classified information on government contractors. Matt and Nick have to get their friends out of the hospital before they are discovered to be American operatives and the oil company realize that their activities are under scrutiny.

Matt, Marge, Benny and Nick plan a trip to experience some white water rafting. On the way there the car develops a fault and they have to limp there way to a nearby small town, Bent Copper, Colorado. They find a garage, with an extremely helpful attendant/mechanic, and while waiting for his diagnosis take a look around the place. Their first impressions are that something is wrong here. They are not sure what, or even why they have this feeling, but they trust their instincts and decide to investigate.

A top Chinese agent, known only as the White Dragon, breaks into a French laboratory and steals a top secret serum that can cause heart attacks and remain undetected. Fingerprints of the White Dragon lifted from the scene of the crime turn out to be that of an American, and the father of one of the team. The SOF team are sent in to recover the serum and capture the White Dragon.

After a couple of US government satellites go down over the amazon NASA send in a team of techs to investigate and find what is causing the failures. When their team has been out of contact for two weeks it is the turn of the SOF team to be called in. They are dropped in to the amazon with orders to find out what happened to the team and the satellites.

A high level mole in the Pentagon has been passing on top secret info and compromising missions. They have also managed to place enough evidence to prove that it is Trout who is the mole. Trout comes out of hiding to ask Matt if he and the team could help clear him and find the real mole. When they manage to capture a woman who could be the real mole she tells Shepherd and the rest of the team that Trout has been using them for his own agenda and not on government authorized missions. They are divided over whom they believe, could this be the end of the Special Ops Force?