Plots
Higher Institute of Villainous Education
After realising that government funding which keeps the orphanage from closing is being cut, Otto Malpense creates a remotely-controlled device that can hack a teleprompter and cause it to hypnotize whoever looks into it. Malpense created the device to embarrass the Prime Minister during a speech. After achieving his objective, he is ambushed and stunned by Raven (an assassin who works for H.I.V.E) and awakens to find himself in a helicopter across from a stranger. The stranger is Wing Fanchu, and they quickly become friends. When the helicopter lands, Otto is informed that he will spend the next six years at H.I.V.E. Dr. Nero, H.I.V.E's headmaster, is interested to know that it took more than two shots from Sleepers (knock-out weapons designed to replace tranquilizer darts) to capture Wing –enough to send a normal boy into a weeks-long coma. He expresses his concerns to Raven and asks her to monitor Wing and Otto.
Otto's skills have identified him as an Alpha: a future leader. He has no intention of staying in this new prison, but becomes friends with others who have been brought to H.I.V.E., including Laura Brand, Shelby Trinity, Nigel Darkdoom, and Franz Argentblum. Otto teams up with Wing, Laura, and Shelby to hatch an escape plan. They travel through the hidden parts of the school, but as they nearly reach their freedom Dr. Nero reveals that they have been on an impossible mission. Nigel stirs up trouble when an enormous, flesh-eating plant (named Violet) he has accidentally bred escapes from the hydroponics lab. Everyone (including the students) jumps into action to successfully save the school, but Dr. Nero and many others are injured. Otto and Wing have a small window of opportunity to leave the school forever, but at the last second they decide to stay. Number One, Dr. Nero's boss and leader of G.L.O.V.E., has plans for Otto Malpense.
The Overlord Protocol
When Wing learns about his father's death, he selects Otto (supervised by Raven) to accompany him to the funeral. Before they can go, the trio is attacked by mysterious assassins. Wing appears to be shot by Cypher, a member of G.L.O.V.E. who wants to seize power and close H.I.V.E. Otto and Raven barely escape and hide in one of Raven's numerous safe houses, awaiting instructions from Dr. Nero. Raven tries to discover what Cypher is up to, with Otto at her side. They discover that the entities they battled at the original safe house are robots engineered for combat. Cypher attacks H.I.V.E., threatening to kill the students to get what he wants. Wing is found alive, shot by a tranquilizer disguised as a bullet, and joins his friends to save the school. They win the battle; Cypher is wounded, and Nero insists that he appear dead to everyone but himself and the doctor who treated him. Otto and his friends learn that Cypher is Wing's father, which explains his kidnapping of Wing. During Dr. Nero's interrogation, Cypher says that his motive for attacking the school was the Renaissance Initiative project. The initiative seeks to recreate Overlord, homicidal AI that wants to kill everything on the planet. Cypher believed that with the Overlord Protocol –a device allowing him to hack everything on the planet –and H.I.V.E. as hostage, he could attack the Renaissance Initiative (which is led by Number One). Otto and his friends are glad to be out of danger and home for good, excited that the H.I.V.E. mind's personality is restored.
Escape Velocity
Nero is kidnapped by H.O.P.E,, the Hostile Operative Prosecution Executive (a new anti-terrorist organisation), and the Contessa becomes headmistress of H.I.V.E. with an elite guard known as the Phalanx. Otto, Wing, Laura, Shelby and Raven are escape from the school after being extracted by Raven and join forces with Diabolus Darkdoom, Nigel's supposedly-traitorous, dead father, who takes charge from a massive submarine known as the Megalodon. Overlord, inside Number One's body, is behind the plot. Otto is Number One's clone, designed as a host body for Overlord. They assault H.O.P.E to rescue Nero, but are captured and sent into space to Number One's hideout. Otto narrowly escapes being taken over by Number One/Overlord, and must delete H.I.V.E.mind. H.I.V.E. is under attack by executioners known as the Reapers, the teachers are shut out of H.I.V.E.'s systems, and the Contessa sacrifices herself to save the school by igniting a pool of jet fuel.
Dreadnought
The arrival of new student Lucy Dexter confuses the students, but they quickly befriend her. On their way to a training mission, they visit the Dreadnought (a new mobile command center for G.L.O.V.E.) The mission is cancelled when the Dreadnought is attacked by a rogue G.L.O.V.E. member. Nero, Raven and the students narrowly escape, but Diabolus Darkdoom is left behind and enemy agents are sent after them. They discover that Lucy is actually the Contessa's granddaughter and can control people with her voice. They try to rescue Diabolus and foil a plan to use American weaponry, controlled by Air Force One, to erupt a supervolcano and destroy civilization. They rescue Diabolus, but Otto must stay behind on the out-of-control Air Force One to disarm the weapon. He passes out after the plane crashes, leaving him in the custody of the U.S. government. Trent talks to the president, and injects Otto with Animus Fluid.
Rogue
Otto has been infected by Animus, an organic supercomputer which can be programmed by H.O.P.E. to make him do their bidding. With Ghost, a superhuman assassin, he attacks members of G.L.O.V.E. Raven is on a mission to find Sebastian Trent, first going to a facility where there might be information. She threatens Khan, who begins to unlock his computer. As he is entering his password, he is killed by a remotely-controlled microexplosive device in his skull. She takes his laptop, and Nero picks her up for the G.L.O.V.E. council meeting. At the meeting of the remaining G.L.O.V.E. members, who are waiting for Darkdoom to fail, Darkdoom is pressured to make a decision and issues a capture-or-kill order for Otto. During a private meeting with Nero, Raven sees a sniper (Ghost) and barely saves Darkdoom from assassination. While Darkdoom is in the H.I.V.E. medical center, Professor Pike and Laura Brand try to fix the school's technical problems. Raven hacks Khan's laptop with Professor Pike's help, and finds a picture of a seed. After consulting the biotechnology teacher, she learns that the seed is most commonly found in the Amazon. Wing (who wants to find Otto) stows away with her on the Shroud, but they are captured by H.O.P.E. Amidst chaos at H.I.V.E., Nero brings in another expert on artificial intelligence (the newly-freed Cypher) to help investigate. They believe it is Overlord, but it is H.I.V.E.mind rebuilding himself. Organic supercomputers repair themselves as seed programs and, when they reach the self-awareness stage, they can exert control. Raven's original purpose for going to the Amazon was to seek help from an old friend, who betrays her. Carlos Chavez, the ruler of Brazil, had pinpointed Raven's arrival. Chavez had enlisted a commander, Rafael, but Raven and Wing defeat Rafael's men and Raven cuts Rafael's throat. After the mission's failure, Chavez (defying Nero's wishes) posts a priority-one notice on GLOVE.net for Operation Raven: to kill Raven. Lin Feng had supported Chavez's assassination attempt on Raven to prevent Nero from gaining power because Lin Feng knew that Chavez was too unruly to control the council, and Lin Feng would eventually take over G.L.O.V.E.
Cypher takes advantage of his freedom to look for Wing at H.O.P.E.'s base, accompanied by Laura, Shelby, and Lucy as hostages he took when he escaped. The girls escape from him and free Raven; when Otto begins to resist Animus (when he was told to kill Wing), Wing escapes to join them. Otto distracts Ghost; Raven beheads Ghost, but Cypher finds the group and tries to kill Otto to protect the world from Overlord. Cypher is shot dead by Wing and Otto is nearly taken over by Overlord, but Laura uses the neural pulse device to eject Overlord and Animus from his system (nearly killing Otto). Sebastian Trent attacks them, but is taken over by Animus and killed by Raven. The students return to H.I.V.E., where Otto recovers and tells Nero that Animus tried to destroy organic material; with the Overlord (not H.I.V.E.mind, as Otto had hoped) seed growing in him, they fused to become extremely powerful. Every time Otto tried to hold them back, he weakened.
Because Darkdoom believes that his old idea of ruling with respect was not good enough and his injuries need more time to recover, he suggested that Nero take over G.L.O.V.E. and add the fear that Number One had. During their virtual meeting, with only nine members (including Nero) remaining, G.L.O.V.E. was in peril. Nero proposes himself as the leader, but Lin Feng opposes him. With no other ally (because Raven killed Chavez), Lin Feng angrily leaves the council. He is part of The Disciples, and talks to Pietor Furan about what happened. Furan orders Lin Feng to apologize to Nero and regain his seat in G.L.O.V.E. Furan then tells Dr. Creed (whom he saved from the rainforest) to perform an autopsy on Trent, who has been dead for two weeks. It is believed that the Animus would be inert, but it emerges and consumes Dr. Creed; the Overlord-Animus combination survives in the doctor.
Zero Hour
Overlord has developed the power to move from body to body if the host has been exposed to Animus. Lucy and Otto share a moment, which makes Shelby laugh and Laura jealous. New machines have been developed, and their first exposure to the public evokes terror as Overlord takes control of the facility (an Advanced Weapons facility in Colorado). Raven is exposed to Animus, and is controlled by Overlord. When Raven, Furan and a team try to capture Otto and his friends, they board Darkdoom's Megalodon ship. H.I.V.Emind is transferred to Otto's mind, since Raven shut off H.I.V.Emind from the rest of the school.
They are attacked by the U.S., which is trying to also capture Otto because Overlord is holding several strategic hostages. Nero, Otto, Wing, Laura, Lucy, Shelby and Laura go into the GCHQ (Echelon) to transmit a signal which activates Zero Hour. Otto secretly installs a destroy code for Echelon, which they accessed through the prime minister (one of Nero's former students). The prime minister (a Disciple) betrays them at the last minute, telling Overlord where Otto is. Raven takes Otto, Lucy and Laura aboard and brings them to AWP, where Overlord is.
Overlord plans to take over the world with self-replicating nanites mixed with animus which, if released, will enslave everyone. The battle is almost over and the Disciples, followers of Overlord, are winning. Nero and Darkdoom must activate Zero Hour, their final effort, in a fight to the death. Zero Hour involves all of the most successful ex-Alphas, outfitted with new machinery and gadgets. They fight, and Lucy sacrifices herself for Otto. Overlord releases the nanites; Otto uses four nuclear missiles to obliterate the facility and destroy the nanites, permanently closing Echelon in memory of Lucy.
The heroes survive; although Overlord is gone, the Disciples remain. Nero disbands the ruling council of G.L.O.V.E, telling them that they are part of a bygone era. This angers them, and some join the Disciples.
Aftershock
The former members of the G.L.O.V.E. council, angry at Nero's decision to replace them, join the Disciples in the Hunt (a plot to sabotage the H.I.V.E. training program). Nero does not know this, and has underestimated his opponents' cunning and resources. Chief Dekker, H.I.V.E.'s new chief of security, is a member of the Disciples who threatens to have Laura's family killed if she does not help him. Laura persuades Otto and the others to help her find the location of the Hunt.
When the Alphas set out for the Hunt, the Disciples are waiting for them. They kill fifteen Alpha students and kidnap the rest, including Laura, Nigel and two new students, Otto's old friends Tom and Penny. Anastasia Furan, the new leader of the Disciples and a ghostly character from Raven's past, bring them to the Glasshouse (an assassin-training facility). Otto, Wing, Shelby, and Franz escape and return to H.I.V.E., but Otto is expelled for his role in stealing the Hunt's location. Dr. Nero makes an agreement with Otto: if he, Raven and H.I.V.E.mind can track down the Disciples, he will be allowed to return to H.I.V.E. Raven and Otto travel throughout Europe to assassinate the Disciples.
Deadlock
Otto and Raven are desperate to rescue their friends from Disciples leader Anastasia Furan. They must find the Glasshouse, the prison where Furan trains children to become assassins. Otto is also being hunted, and the three months Otto has spent away from H.I.V.E. have given the Artemis Section (an elite American intelligence division which reports only to the president) an opportunity to locate him. Tom dies after an escape attempt from the Glasshouse, but they send their whereabouts to H.I.V.E. Anastasia has spent years trying to create Zero, a clone which looks like Otto, that Otto kills with the help of H.I.V.E.mind. The Glasshouse is destroyed, and Nero locks Anastasia under H.I.V.E. Otto and Laura kiss. Zero had hinted at more clones, and about a dozen cloning vats (each with a clone of Otto) are counting down.
Bloodline
A99A, a clone of Otto, controls Dr. Higgs. The clone renames herself Anna, and intimidates the research team into continuing making her clones. Anna forces Joseph Wright, a Disciple, to locate Anastasia. At H.I.V.E., Professor Pike accuses Otto of attacking H.I.V.E mind; in the control room, they find that Anna is the attacker. H.I.V.E mind fails, and Anna controls the school. She can control a person with her voice (characteristic of the Sinistre family) and shares Otto's ability to interface electronics. Nero, Otto and his friends barely escape with the help of Darkdoom and his new submarine, also named Megalodon. Nero, Darkdoom and Otto visit the Queen, the last survivor of the Sinistre family. One of the security teams works for the Disciples, who send a squad. The Artemis Section also finds Otto, and sends fighter jets and a team of Navy SEALs.
Nero suspects that the Queen is involved with this; Anna's voice is exactly like hers. She denies any involvement, and is angry to learn that the Furans have used her voice. The Disciples and Navy SEALs team converge and invade the house, and the Queen is forced to lead them to a secret passageway leading to the roof. Otto and Nero escape in a helicopter which crashes; Nero is captured by the Disciples, and Otto by the Artemis Section. Darkdoom and the Queen escape in a Shroud, a stealth helicopter from the Megalodon. Nero is held at H.I.V.E. and tortured by Anastasia and Raven. Otto is questioned by the president, who initially thinks he is responsible for Anna's hacking of the global surveillance programs (which causes a Russian ship to disappear). The president shows Otto that they have a bit of Animus, which Otto thought had been destroyed in Zero Hour. Darkdoom and Otto meet and develop a plan to defeat Anna. The plan (a trap) goes horribly wrong; Darkdoom's men are killed, and Otto is captured. At H.I.V.E, Wing, Mrs. Leon and Penny evacuate the school by launching the students into the volcano and the volcano into the ocean and the surrounding area. During the widespread disruption, the robots which survived Cypher's attack and were being used by Anna are short-circuited.
Otto confronts Anna, pulls out the Animus, injects himself, and traps her. Anastasia forces Raven to torture Nero, and kills the Queen. After the Queen dies Nero finds out Raven is his daughter and, when Anna is killed, has Raven kill Anastasia. Otto kills Anna's clones by purging their tanks and Nero, Otto's friends and the teachers board a Shroud and await him. It suddenly takes off, and Otto says that the Animus is killing him. He apologizes for betraying them and thanks H.I.V.E mind. H.I.V.E mind kills him, and transfers him to one of Anna's clones; in a year, he will be reborn. The volcano explodes as H.I.V.E mind detonates a small nuclear bomb at its base. Otto's friends mourn him, and it is unknown if H.I.V.E mind survives. At the end of the book a reborn Otto appears on Laura's doorstep.
