In Port Elizabeth, Dr. Miami has an encounter with Karen Low, and by learning that she is unemployed, she decides to hire her as a bodyguard. Some time later, the duo has a meeting with Koko's team at the Solomon Islands to oversee the launch of the final item of HCLI's satellite network designed to give the company and their affiliated arms dealers an upper hand against their opponents. On a later occasion, R has a meeting with George Black and informs him that Koko knows that Dominque's team was hired by the CIA. Black claims that it was not his doing as his true intention is to make of Koko a tool at the behest of the U.S. as part of his plan called "Operation Undershaft", which involves R's undercover assignment. Meanwhile Hex, the CIA Special Activities Division operative behind the assassination attempt in Egypt and an old enemy of Koko's, learns from a fellow CIA agent the details of Operation Undershaft and wonders how she can hit Koko where it hurts the most before killing her.

A flashback shows how R, whose real name is Renato Socci, met George Black back in the 1990s with the Balkans under UN intervention before Socci works with Black to infiltrate HCLI after the two worked together to hunt down war criminals. Another one shows how Hex was in Operation Undershaft when she was recruited from the disbanded Wide Range Communications Platoon to the Special Operations Group of the SAD, leading black ops missions against arms dealers, including Koko. Koko has a private meeting with Amalia about George Black and his quest to put arms dealers under his thumb for the CIA. Meanwhile, Koko gives her team new weapons to replace their personal weapons while conducting VIP protection exercises. Koko asks R about George, which R tries to tell Koko a little bit of the truth to hide his cover. Later on, R contacts George and persuades him to remove Hex from the operation without any luck. George however, knows that Hex's next target is Jonan and does not refrain from have him sacrificed to keep her under his control.

R convinces George to tell him the location of Hex and her SOG team and rushes to help Koko and Jonah, finding them already under attack from them. After revealing to Koko that he is a spy under George, he manages to have both evacuate to safety and confronts Hex head on. When the two exchange shots, R and Hex manage to hit each other's left eyes, with R's wound being fatal. After the rest of Koko's team reaches the scene and takes down the snipers giving support to Hex, she is forced to give the order to retreat. Upon learning of R's death, and enraged Koko contacts the HCLI and demands them to track down Hex's location. Some time later, Hex and her two remaining men, sheltered in a cave on Northern Iraq, see a B-52 bomber sent by Koko that carpet bombs the area. R is buried on a scenic view near the coast and George appears to pay his respects, having a short meeting with Koko and her team in the occasion. Just before leaving, George learns of Hex's death and hearing the voices of R and Hex remembering him about how they warned him to not underestimate Koko, he decides to not give up on her.

In Jakarta, Kasper and his team find themselves once again outsmarted by a rival Japanese company and he decides to take the fight to them with Koko's help. Still coping with the loss of R, Koko and her party travel to Japan while Kasper sends a message to the Japanese by having some of their men killed. When Koko makes the rendezvous with her brother in Japan, Jonah asks him to show him how the three children he asked to give shelter are doing. Kasper brings Jonah to where the three are living but he decides to not meet them, being satisfied for just knowing they are doing well. As the Japanese learn about the death of their comrades, Kaspar questions Tojo about Hinoki Yousuke, his former superior in the Japanese Ground Self-Defense Forces, the man leading the team.

As Kaspar returns to Jakarta, Tojo debriefs his comrades at the Narita International Airport and informs them that the Special Research Unit (or SR Unit) of the Defense Intelligence Headquarters are responsible for harassing Kaspar's operations in Southeast Asia. He also informs them that the unit was created due to American requests during the Vietnam War, which evolved into a dummy corporation named Ganville Trading. Col. Hinoki informs Koko of a rendezvous point for the two parties to meet with the pretense of discussing a mutual agreement, but Koko warns her team to prepare themselves for the worst. In Jakarta, Kaspar meets with one of Ganville Trading's employees named Kurosaka, who takes the opportunity to attempt to kill him, but is stopped and killed by Chiquita. Now knowing that the enemy set a trap to them, Kaspar and his squad make their way to evacuate, confronting the SR Unit commandos along the way.

Jonah was able to escape death after informing Koko that the supposed rendezvous point was empty at Tokyo Bay Aqua Line's Umihotaru, avoiding an ambush. Koko and the others were able to get away, managing to defeat the remaining SR Unit operatives. When Jonah, Koko and Tojo meet with Col. Hinoki at the Bahamas, the ex-SR Unit officer told Tojo that he allowed the remaining SR Unit operatives to take on HCLI because he noted that they needed to fight one good battle against Koko and Kaspar. Hinoki also explained that the unit was becoming arms dealers themselves, something that the colonel did not wish to happen as circumstances gave him no choice but to let the unit destroy itself as they lost its true purpose, which was to be a black ops unit of the DIH. In a flashback, Tojo remembers leaving the SR Unit because the unit was turning its back on its Cuban agents during a black operation, which made Tojo resign after returning back to Jakarta. This eventually led to his recruitment to HCLI under Kaspar before he joined up with Koko.

While driving a convoy through Iraq, the team hear the story of how Wiley met Lehm in Iraq during the first Guld War before he got hired by Koko's team, when the members of PMC Excalibur are fired by Koko for shooting a passing vehicle without even checking if it was a threat or not, but their interpreter Nazar offers himself to accompany them on their Iraqi trip. Wiley makes use of his demolitions expertise to figure out a trap set by Excalibur and the team successfully repels their pincer attack, especially when Nazar, who was supposedly working with the enemy switched sides, collaborating with Koko instead.

Koko's team has a meeting in England with doctor Minami which brings up Schokolade's atention. She contacts Scarecrow who informs Bookman about it. Minami takes Jonan and Karen for a butterfly hunt and Jonan asks her about what she and Koko are truly planning, but she refuses to respond. As she bids farewell to Minami, Koko agrees with her idea to give a name to their plan which from then on is called "Jormungand". The members of CCAT have a dinner with Minami and ask her for a role in her and Koko's enterprise but she refuses and Curry considers quitting the arms dealer business. Some time later, Amalia Trohovski visits Koko claiming she wants to join HCLI as well. As Amalia displays to Koko the newest UAV technology she obtained, Kasper makes an announcement on Phillipines of HCLI's satellite network, the "Hekmatyar-Global Grid" or simply "Hek-GG" which according to him, will help their clients arround the world to greatly improve their logistics. Bookman and Hinoki react coldly to the announcement and Jonan realizes that Koko does not seem interested on it at all and keeps talking with Amalia instead as he ponders that despite having traveled with her for so much time, he has not yet realized her true character.

In the Caucasus, quantum optics expert Elena Baburin is kidnapped by Koko's team and brought before her. Meanwhile, Scarecrow is informed that Koko has been pooling all her resources in a factory in South Africa in secrecy, a move she is concealing even from HCLI. After closing some deals around the world, Koko and her team is approached by Hinoki and Bookman at the Washington Dulles International Airport to remember her that she is being watched. When Schokolade, who was following Koko around the world informs Scarecrow that she had lost her track, Bookman realizes that Koko's next move is to extract Leila Ibrahim Faiza, aka "Rabitfoot", a quantum physicist, hacker and online activist from the Guantanamo Bay detention camp as according to the intel about her recent activities, Koko's secret project involves building a Quantum Supercomputer and she needs Rabitfoot's help to complete it. Meanwhile, Koko's team is preparing themselves for the kidnapping when Lutz questions Koko about her true intentions. Although she refrains from answering, all her bodyguards including Lutz reaffirm their commitment to her. As Hinoki discusses with an NSA officer about the kidnapping, he is informed by him that Bookman already contacted the NSA about it, and Rabitfoot is about to be transferred to another detention facility under some heavy escort whose orders are to kill whoever tries to rescue her.

After successfully managing to kidnap Rabitfoot and flee to the woods near the Cuban border, Koko's team find themselves in a pinch against the "Night Nine" who is dispatched after them until Koko manages to shot down their surveilance UAV and make use of her new system to hack into the U.S. military to feed their enemies with false info which guides them near a Cuban base, providing an opening for her comrades to escape. While traveling in a freight to South Africa to rendevous with Minami and Elena, Koko convinces Rabitfoot to work for her and finally reveals to Jonan and the others the true nature of her plan once they reach their destination. According to Koko, the quantum supercomputer and HCLI's satellite network together form the "Jormungand" system, which she will use to take control of the world to prevent further wars. She also confirms that her next step is to make use of Jormungand to impose a worldwide aerial blockade, disabling all civilian and military aircraft along all air weaponry. However, after Koko reveals that all airplanes in mid-air will inevitably crash when that happens, causing hundreds of thousands of deaths, a desperate Jonah draws his weapon in an attempt of dissuade her.

Claiming that her plan is already past the point of no return, even if he kills her, Koko convinces Jonan to put down his gun, but he can't decide about joining her or not and flees away instead. Jonan is found and picked up by Kasper and asks him for a place in his team. Bookman is contacted by Koko who asks him to meet her in North Africa, but just as he arrives there, he is ambushed by a local army, just to be rescued in the nick of time by U.S. troops, realizing that it was all orchestrated by Koko to demonstrate him the true range of her newfound power. As Jonan travels arround the world with Kasper and Chiquita, now as part of their squad, he wonders about what to do next.

Two years pass and with wars spreading through the world, just as Koko predicted, she still has not activated Jormungand yet. Kaspar, who already figured out Koko's plans, instead of trying to stop her, agrees to protect her as she launches into orbit a compact version of the Quantum Computer at a cosmodrome in a restored Soviet Union, putting it out of reach from her enemies. Just as he is leaving with his team, Jonah asks Kaspar permission to leave, to which he agrees, claiming that he will keep his part of the bargain of protecting his friends in Japan while giving him a passport and a Swiss Bank account as a parting gift. Four days later, Jonah wanders through Azerbaijan where he is found by Koko and her team. Having welcomed Jonah back into her party, Koko activates Jormungand.