It is a new term at St. Heart's and with Zoe still away, spy handler Frank tasks the team with the mission of tracking down one of Zoe's remaining duplicates, Keri, who is the new intended host of The Mastermind's consciousness. It becomes a race against time to reach Keri first and save her from the clutches of KORPS.

Keri's first mission as a fully-fledged M.I.9 agent comes sooner than anyone expected when the team discover an abandoned KORPS base beneath the school playground. Keen to investigate, their efforts are repeatedly hampered by the Saint Heart's centenary celebrations. As a terrible storm closes in, Frank begins acting strangely. When they finally uncover the truth about KORPS' long-forgotten experiments to create monstrous Super-Soldiers, they worry that it is too late to save their beloved boss and prevent the fancy dress disco becoming a Gothic horror nightmare.

The team are sent to investigate Derren Beige, a flamboyant clairvoyant whose previously pathetic predictions have suddenly become scarily accurate. But Derren is kidnapped from right under the agents' noses, leaving M.I.9 boss Stella far from impressed. Suspended from duty, the team must race against time to figure out how Derren uses drawings to predict the future, then rescue him before his new-found powers fall into the hands of his dangerous captives.

When government food advisor George Monoblot is sacked after highlighting the dangers of a revolutionary sugar substitute, Cupodium, he seeks retribution and unleashes a virulent form of the substance into the food chain. The team must find the antidote and stop Monoblot before the school and whole country is affected and subsequently destroyed by the final stage of the compound - Rage.

During a successful M.I.9 mission to secure the deadly assassin Samantha Stiletto, KORPS mistakes Keri for the assassin. Keri takes Stiletto's place in the world's most deadly tournament, The Shadow Games, where the winner will become the new Shadow Master of SKAPULA, KORPS' assassination division. The team's only chance of rescuing her is to rely on ex-Shadow Master, Alexis von Hades, who is far from trustworthy.

Tom discovers the online Dark Wizard avatar from Blade Quest has become self-aware.

Dan joins a free running group that has been accused of committing crimes. Stella goes undercover on a teaching job for Saint Hearts.

Frank is asked to join a secret order within M.I.9 called the League of Mata Hari. However, the curious team uncovers a criminal conspiracy that runs throughout M.I.9.

M.I.9 have acquired a fragmented message from the terror organisation 99p. They are a group that is dedicated to bringing down the world's economy to 99p. The message reveals that the group is going to attack the M.I.9 Communication Centre and Dan, Aneisha and Keri go to investigate but are attacked by the group. After managing to escape, the team question how 99p managed to find the centre. An external breach is to blame, leading the team to believe that Scraper Associates are at fault, being the only non-M.I.9 personnel to have access to facilities. Meanwhile at St Hearts, after having many billboards installed, by the same Scraper Associates, Mr Flatley and the students try to come up with an advert to promote their school.

Mandy Pluckley, the country's top 'agony aunt', has been abducted by KORPS. She is the sworn confidant of the Prime Minister and he is dependent on her. Without her guidance, he has started to lose his mind and sense of reality. Making matters worse, in three hours, the British Government is holding the Unity Summit which puts every country's defences under a single system. His only permitted aide is Mandy and the team need to find her so that the PM can complete his duties at the Summit. After barely competing their mission, the PM sees their close call as a danger and orders them to be stood down, permanently. Meanwhile at St Heart's, Mrs King is shocked when she receives a letter informing her that a student has complained to the Education Minister about her. She vows to find the culprit no matter what.

The MI High team have set up their own agency after being fired from M.I.9. After many unsatisfying missions and almost quitting the job completely, they get the call they've been waiting for. Edward Lambsbottom, a senior technician at GDHQ (the government's secret listening station), has intercepted a conversation with the Crime Minister. She was discussing KORTEX and that KORPS are planning to assassinate the Deputy Prime Minister. He tried getting this information to M.I.9 but saw his new boss, Martin Strong, destroying evidence. The MI High team take this information to Frank, who still has a job at M.I.9, to try and figure out what's going on.

The team, Frank, and Stella have gone into hiding as M.I.9 has been taken over by KORPS. As KORPS' plans are nearing completion, the team must act fast. Frank tells them about 'The Heart', a rumoured super computer that controls all of KORPS' networks. They plan to destroy it but the only problem is that it is located at KORPS Central HQ which has never been found. Tom comes up with an idea and the group break back into their base under St. Heart's. Tom reveals that he made a gadget that contains a microchip that holds an anti-virus before they were fired, it will make Keri reject The Mastermind's consciousness if KORPS try to transfer it. It also contains a tracking device, so if Keri gives herself up, KORPS will take her to their HQ, leading to The Heart. Keri accepts, but the team also have far more pressing matters to worry about. Meanwhile, Evelyn Baxter is bent on taking over the country, and then destroying it.