The men are in Cyprus capturing a rogue agent and brining him in. They successfully complete this mission with no problems and head home. Molly is leaving the home and heading towards her car when she is approached by a strange man. He takes her keys and tells her that her husband is in trouble. At the same time, Kim is loading groceries into her car at the store. Serena runs out into the parking lot, Kim yells for her to stop and a strange man catches her before she is hit by a car. The man introduces himself as Agent Katz, gives Kim his card, informs her on how to verify his identity and tells her that Bob is in trouble. The men return to their bunker to find the MP's there and they are being told not to pass. As the men ready themselves for a fight, Ryan shows up and orders the MP's away. He explains to the men that they are being investigated for criminal activity. He orders them to be available for the investigators and to walk away in five different directions. He further orders there to be no further communication with each other.
Jonas goes into Ryan's office and states, "Nice Show". They talk about what is happening and Ryan states that no one is taking his calls. They realize that the threat is serious and everything is at risk. Jonas goes home to Molly and they talking about what is happening. Jonas goes over their "Rainy Day" plan and pulls out a drawer with passports taped underneath. He also gives Molly a gun. Bob goes home to Kim and finds Agent Katz in his home. Bob is not happy about him being there. He assures Bob that he wants to help him and his family. Mack is at home burning papers, empting bottles of medicine and going through hidden papers. He finds divorce papers.
The men meet with Cheals in secret to plan their next move. Charles provides a wild goose chase to the agents following him and Hector. They decide that they need to get their hands on records of their missions. They determine that the records are in a safe in Ryan's office. Tiffy arrives at Molly's, telling Molly she dropped the girls off at a friend's home. Molly fills Tiffy in on the situation.
As Jonas is coming home, he is approached by a man. When Jonas questions him on who he is, the man refuses to identify himself to Jonas. Molly comes out of the home and tells Jonas he was the man that approached her. Jonas tells the man to stay away from his wife. Tiffy is at home packing when Mack comes in. He is very angry and accuses her of trying to run away with Wilson. She explains that she is packing the family for them. Mack tells her that he found the divorce papers. She explains that those were drawn up last year and she never filed them. They continue to argue about Tiffy's alleged affair and she tells him that she did not sleep with Wilson. She does tell Mack that she was tempted. Mack grabs her and pushes her against the wall; Tiffy runs into the bathroom and shuts the door. Mack is furious and bangs on the door. Tiffy emerges from the bathroom with a gun, Mack easily disarms her. They continue to argue and fight. Tiffy grabs a razor and cuts her face. She states that she could tell people he did it and they would believe her. Mack can not believe that she did that and reaches for her to help. Tiffy pushes him away and runs out of the home.
Hector, appearing intoxicated, heads towards the commander center and the MP's on guard. He attempts to talk them into letting him into the building. They refuse and he assaults them and gets arrested. While they are taking Hector to the Brig, Bob and Jonas break into the headquarters. The enter Ryan's office and located the secret safe. Bob breaks into the safe to find it empty.
Ryan is at home with the documents and is mailing them to himself all over the world. His wife questions him on his actions. Ryan states he is not going to help send his men to prison. She wants him to cooperate with the investigators; he states he will not betray his men. Tiffy went to Molly's and Molly and Kim are treating her cut. She tells them that she does not know why she cut herself, she was just so angry. Molly and Kim question Tiffy on if Mack did it and Tiffy stands firm on she did it to herself. Kim encourages Tiffy to leave Mack, noting that this is a good time because of everything else going on.
Ryan reports to the General who tells Ryan that he his relieve of duty. The General believes that Ryan failed in his duty to lead his men. Mack, Jonas, Bob and Chelas meet again in their secret place. They note that Hector is being held in the drunk tank and they are worried about Charles, no one has seen him since he lead the wild goose chase. They conclude Ryan must have moved the documents and there is nothing more they can do. Cheals notes that the league will help each man out whether they stay and fight or leave and hide. Jonas notes that each man must make his own decision and that this will be the last time they meet.
Jonas heads to the bank and requests a change in his pay status; he wants all but $50.00 of his pay to go to his wife. The Sergeant tells him his account has been flagged, but that it is his money so she changes it for him. Bob and Kim are discussing their options. Kim notes that Tiffy left, Grey's gone and Mack is chasing shadows. They discuss what Bob should do. Kim wants him to seriously consider the CIA's offer because she thinks this offers her, Bob and there kids safety. Bob is not convinced.
Mack, Hector and Bob are brought in for questioning by the Generals and Colonels. They tell him he will be confined unless he gives up Jonas and Charles. As they escort Mack out of the room, he does not salute. One of the Generals notes that Mack did not salute and Mack's response is that he has no superiors in this room. Hector refuses to make a deal. Bob is brought in and asked for an answer regarding working for the CIA. Bob states he needs more time and they state they need an answer now. Ryan and his wife are again discussing his position on this matter. She asks him to cooperate with the investigation and obey his orders, if not for himself then for her. He states he can not betray his men and she leaves him.
Molly comes home to find her home ransacked, a bloody hand print on the wall and no Jonas. She calls Ryan, who does not pick up the phone is drinking, listens to Molly's message and picks up his gun. Crime scene investigators and the CIA turn up at Jonas' home. Cheals runs interference for Molly with the agents by telling them they need to go through him to talk with Molly. He passes a note to Molly and explains that missing is an active duty on the pay scale. Once inside Molly looks at the note and it is a bunch of numbers. She grabs the book, Paradise Lost and works on deciphering the code. The note states, Arrived Safely, Be Strong, Love J.
We see Jonas getting off a bus in Panama City. He heads into a cantina, trades coins with the owner and goes upstairs with one of the girls. Jonas meets with Doyle who provides him with a new identity, a new passport and a gun. He explains the procedures to Jonas. Hector and Mack are locked up and Bob is home with Kim discussing what has happened. Kim wants to go and Bob states he won't betray his friends. The following day Bob meets with Agent Katz and Bob gives him a paper. Bob tells him he wants his wife and children off the base. The CIA wants Bob to find Jonas Blane. Bob asks what if he doesn't and their response is then you will go to prison with your friends.