Ed and Beckett go 'under cover' and end up on board a submarine. They are, however, found out to be fakes and, whilst Ed escapes, Beckett is left on the submarine with a money hungry man, eager to gain access to a bank and steal some diamonds a long the way. Beckett ends up getting trapped on the submarine, as it slowly fills with water. The man, meanwhile, has got his associate to steal these diamonds, but their plan is foiled when Ros enters the scene. Ed goes under the sea to search for the submarine and but will he find Beckett in time?

R-6 is a new type of metal, and it has an explosive nature. A man called DaSilva decides to take advantage of this property of the metal and tries to steal it. The Bugs team are involved and try to stop DaSilva leaving the country with the metal to make it into deadly weapons.

A special formula has been developed which enhances the performance of athletes. However, no-one has considered the after effects, which are that when the person's heart reaches a certain rate, the body can't cope and the person drops down dead. Ed comes to realise this when he is having a karate match with a person who has been injected with the stuff, and the man goes hyper, then falls down dead (whoops!). Ros eventually goes to find out more about the stuff, and ends up with another hyper person chasing her, then he suddenly collapses. however, Ros is still caught and taken away by the developer of the formula, to be his new guinea-pig.

Many small companies are being bought up by two mysterious men and Ros, Ed and Beckett are called to investigate. When the manager in another company is suddenly blown up, Beckett takes his place. The two suspicious people turn out to be Jean-Daniel and his brother, Patrick. They realise that Beckett is not the real manager and Jean-Daniel goes round to ‘Gizmos' (the place where Ros, Ed and Beckett were based in Series One) Beckett ends up being kidnapped. Ed's friend, Clare, has also got mixed up in the brothers' plans, and her daughter, Katie, has been held hostage until she gives them exactly what they want. Jean-Daniel's brother is killed. Beckett and Katie manage to escape and stop Jean-Daniel's plans, and reposition the missile that stops any type of computer generated items from working, to where they are.

Ros and Beckett first meet, after Beckett is forced to leave The Hive when he is framed for leaking information. The real traitor turns out to be Beckett's boss, Cottrell, working alongside his lover, Elena Johnson. The pair are trying to steal SACROS, a device which jams satellite signals. Beckett, Ros and Ed race against time to save Beckett's job and SACROS, and to stop Cottrell and Elena.

Ros, Ed and Beckett's first customer appears in the form of Irene Campell, who turns out to have conned Beckett into helping her continue doing her business. Roland Blatty, a friend of Ros' who own the new Bureau of Weapons is trying to put a stop to the devices Irene sells, which have killed countless people. The team race against time to stop Irene and her legal adviser, Morasco and at the same time save Ed from a microbe that is killing him.

Ros, Ed and Beckett are called in to investigate the mysterious plane that went ‘out of control' for a while. However, while Ros is checking out the aeroplane, it suddenly decides to take off!!! Ros is left in the plane and it takes off, and Ed and Beckett discover that there is a man behind it all, controlling the plane like a remote control one. Ros starts to panic as the fuel gradually gets lower and lower, and Ed goes to find the man behind it, telling Ros that she might have to land the plane herself.

An attempt to steal a revolutionary new car with an advanced guidance system is foiled by the Bugs team. The thieves then turn their attention to a millitary vehicle powered by a radioactive RTG, and Ros and Beckett have to cliumb onto the moving driverless vehicle, to stop the explosion from breaking the radioactive container and killing off most of the people in the country.

Ros, Ed and Beckett are called in to protect Anna Fabrizi, a visiting Italian politician who has vowed to fight political corruption in her country. Ed takes on the role of the man hired to kill Anna and he finds himself in a situation where he has to decide between Anna's life and his own...

A new type of food called Phodex has been created and it is made from some sort of algae. Ros, Ed and Beckett are called to investigate about this stuff, and Ros ends up getting trapped in some room, with the oxygen levels slowly decreasing. However, Ed and Beckett realise all is not right when the creator of Phodex tells them that Ros has gone to the hairdressers. They find her just in time and she is OK. However, a short while later, the team find out the secret of Phodex, that it is toxic when exposed to ultra violet light, and Ros ends up eating some contaminated Phodex, and starts to die. There is soon a race against time for Ed and Beckett to save Ros and the other people who have eaten the toxic Phodex, and Ros' condition gradually begins to deteriorate, as her vision goes blurred and she keeps collapsing. However, she manages to save the day, by finding out what the code is to the place that has the antidote. She has to read an electronic organiser, but will she get the passwor