The old M.I. High team have graduated and spy handler, Frank London, is on the lookout for a new bunch of intrepid young secret agents to face a global network of evil enemies. Three teenagers who use their unusual talents for dubious purposes are selected. Signing up for spy duties are: super resourceful action man Daniel Morgan, master of disguise Aneisha Jones and tech genius Tom Tupper. In this explosive first episode, the new team embark on their first mission, intercepting the shipment of SKUL's ultimate weapon. The weapon turns out to be a teenage girl called V:9:5:Z:0:E:6 (who later becomes Zoe), but there is an even deadlier enemy waiting in the wings.

Tempers flare and loyalties are tested when a series of embarrassing incidents threaten to bring down M.I.9. The team suspect a resurgent enemy organisation called KORPS of coordinating a sting against them, but having seen KORPS destroyed ten years ago, Frank refuses to believe that they still exist. The team must figure out if there is an enemy agent in their midst or if they are dealing with a foe more cunning than SKUL.

A mysterious fireball crashes in the woods near St. Heart's. Believing it to be a U.F.O., curious students swarm the crash site which turns out to be an enemy satellite with military base information from across Europe. Mr. Grosse, a government agent in charge of the crash site, is revealed to be an impostor working for KORPS. The team must recover the satellite's black box before it falls into enemy hands.

Shunned by the pop world for not having superstar looks, embittered music mogul Cuthbert Peabody hijacks a new M.I.9 invention capable of changing a person's face. He turns popstar Calvin Lame's latest hit single into a weapon to use against the people who he holds responsible for his failure - pop fans. The team must crack an elaborate musical code in order to stop him, but without a musical bone between them, they must turn to an unlikely ally for help - Byron.

The team are given their first international assignment in the rogue state of Boldovia where the local secret service has developed a data mining device capable of destroying M.I.9. On a high octane mission in a foreign land where nothing is what it seems and no one can be trusted, the team must succeed, or risk the destruction of M.I.9.

On a campaign to get kids eating more healthily and concentrate at school, St. Heart's is chosen by celebrity chef Jimmy Jubbly as a test bed for his new health drink - Jubblyade. But Aneisha is quick to discover that it is affecting everyone's behaviour, making them operate with a hive mind.

Out of sync with the times, an old-school spy infiltrates the St. Heart's spybase and hijacks an M.I.9 invention capable of upgrading M.I.9's technology. Once she reverses it, she offers Dan the chance to join the 'old school spies'. With the world's technology being downgraded at an alarming rate, the rest of the team must convince Dan to change his mind, and reverse the damage.

Funded by KORPS, scientific genius Bobby Bleach has brought the country to its knees by releasing a plague of airborne supergerms which have incapacitated everyone who breathes them in. Tom is the only member of the team who escaped infection, and must overcome his fear of being in the field and stop Bleach before it is too late.

Top secret scientific components are being stolen by a thief dressed as a character from a best-selling series of fantasy novels. The team go undercover at a fantasy convention only to discover the threat is far greater than they'd anticipated. Someone is plotting planet-wide destruction in order to make the post-apocalyptic world of the books a reality. Dan must put his faith in the power of imagination to defeat the evil Dark Wizard.

After being haunted by memories of a terrible decision which cost the lives of his entire team in the final battle with KORPS over ten years ago, Frank is sent to a nightmare treatment centre to prevent his sleepwalking from blowing his cover. But KORPS have infiltrated the facility and have been stealing government secrets right from the brains of agents. With the threat of nuclear destruction looming, the team are faced with their most difficult dilemma yet - to save Frank's life, or rescue Britain from catastrophe.

Sent to Uttland on the pretense of being on a school trip, the team must break into the country's deepest, darkest prison to help a former KORPS leader escape. But things go awry when their classmates are falsely imprisoned by fearsome prison warden, Arme Gonnersson. The team must jailbreak their entire class without blowing their cover. Zoe discovers from the former KORPS leader that she may be the daughter of The Mastermind.

Briefed to protect Grand Duke Nicholas, the heir to the throne of a small European state who has had kidnap threats made against him, the team hide him at St. Heart's, where the arrogant prince must learn to behave as a commoner with hilarious consequences. During this episode, Zoe is still shaken by the fact that she may be the daughter of The Mastermind. She uses her DNA and finds she has a sister, B:9:2:K:L:O:E:7 (Kloe) who is later revealed to have tampered genes. She's dangerous, and can't become an M.I.9 agent. Kidnapping the heir and demanding 10 million pounds, Zoe must stop her sister, alone. After the mission is over, Frank tracks Zoe's DNA all around the world, and sees that there are many matches. Too many.

Pieces of the jigsaw puzzle begin to fall into place when the team finally discover the grand scheme KORPS has spent the last ten years building towards. Zoe is kidnapped by KORPS and is revealed to be one of the many clones of The Mastermind. KORPS want to put his consciousness inside her brain, believing that she's the only perfect match. The team must find Zoe, and stop the mind transfer.