As Republican nationals make several strikes in London, another bombing at a secret military installation catches the team's eye. Special Branch tracks the entry of a Serbian war criminal while a military convoy is attacked - and the exiles responsible stockpile enough arms to start a small war. While Tom keeps trying to make things right with Ellie, he and the team race to discover their enemy's final target.
An extremist mullah may be planning England's first suicide bombing. MI5's mole is discovered and tortured, leaving the team in need of someone who can get deep inside the mosque. A former Algerian spy smuggles himself into the UK and offers to help - but his loyalties are questioned by Tom. As the mole gets closer and closer, he falls out of contact with the team, leading to a dramatic showdown in a schoolyard - with one child wearing a bomb.
Repeated attacks on MI5's computer system threaten the theft of virtually all classified information. Danny is undercover as a journalist for an socialist paper linked to an anarchist group while Zoe takes a turn as a middle school teacher to get close to another instructor who may be spearheading the computer attacks. Moreso than other episodes, though, everything is not as it seems as a long-dead agent and a potential nuclear device at the school play into a web of deceit and confusion that nearly costs MI5 all their secrets.
Twenty billion in US aid has disappeared from Russia. Meanwhile, MI5 is called in to deal with the theft of a billion dollars from a well known bank - that also handles government accounts. A former KGB officer turned Mafioso is pulling strings in the bank - and possibly in the government - to launder the cash. Danny goes undercover as a commodities trader to find out what the bank and the chancellor's office aren't telling the team. Meanwhile Tom's relationship with the doctor continues to develop, and Zoe gets a pleasant surprise - and then a nasty shock - about her...
A routine MI-5 training exercise to handle external calamities turns sinister when the team finds out that the threat is real and that a deadly biochemical weapon may have wiped out the government and most of south London. Amid the chaos, the team has to cope with the situation in the midst of a near total communications blackout.
The American president's unexpected visit to London forces the MI5 and CIA teams to work together. Harry suspects that there is more to the surprise visit of the American President than the Americans admit to. After some investigations on MI5's part, Harry's instincts are confirmed: the plans of the American President involve a secret meeting between him and the Libyans. After Tom's break-up with Vicky, he is meanwhile facing difficulties from his former girlfriend's revenge plan to hurt Tom.
A French scientist Jerome Durand, has created an air burst EMP missile that when detonated, will shut down all electronic equipment within a square mile. He's now believed to be in London working with a British financier, Frank Hastings, on a possible sale of the new system. The French DGSE send an agent, Jean-Luc Goyon, to work with MI-5 but the British government plans to steal the system before it can be sold to anyone. When Harry Pearce's house is burgled by a gang of professional thieves, they also happen to get away with a briefcase of particularly sensitive ...
Due to a rail strike, the transportation of a load of nuclear waste has to be done by road. Zoe's task is to make sure that the transportation of nuclear waste reaches its destination safely. MI5 receives evidence that a discontented army officer is planning to lead the armed services in a mutiny. Tom is sent to investigate undercover but is convinced he is wasting his time. When Danny arrives to release Tom from the task, his cover is blown and it becomes clear that Major Curtis has attached explosives to the nuclear waste that is being transported by road.
The Chala Cartel, a Colombian criminal organization dealing with drugs and weapons, are the focus of MI5 this time. Trying to get into the country, Chala Cartel kill 8 members of custom. In order to get to the core of Chala Cartel, Tom and Zoe start liaising with the leader's girlfriend Mariella.
Harry finds out that Tom and Christine Dale, a CIA officer, are having a relationship. Tom ignores Harry's demands to end his relationship with Christine. Tom learns that an American assassin has come to Great Britain. This news was not passed on to MI5. Tom doesn't want to compromise Christine, so he is unable to tell Harry what he knows. On Tom's demand Danny and Zoe - without Harry's knowledge - take on the matter but things turn out badly. Tom's strange behavior and the set-up against Tom make him appear suspicious. Zoe and Danny believe that Tom might have gone ...