"Marcus used me to design weapons. I helped him realize his vision of a militarized Starfleet. He sent you to use those weapons, to fire my torpedoes on an unsuspecting planet, and then he purposely crippled your ship in enemy space, leading to one inevitable outcome: the Klingons would come searching for whoever was responsible, and you would have no chance of escape. Marcus would finally have the war he talked about, the war he always wanted."
Khan Noonien Singh, 2259


The militarization conspiracy was a plot orchestrated by Federation Starfleet Admiral Alexander Marcus and a faction of Section 31 to militarize Starfleet for a possible war with the Klingon Empire. To achieve his goals, Marcus used the genetically enhanced intellect of war criminal Khan Noonien Singh. However, Marcus's plans backfired and he attempted to cover up the conspiracy, while trying to start a war.



"I took a tactical risk when I woke that bastard up, believing that a superior intelligence could help us protect ourselves from whatever came at us next. But I made a mistake, and now the blood of everyone he's killed is on my hands."
Alexander Marcus, 2259


Following the destruction of the USS Kelvin in 2233 , the USS Enterprise under Captain Robert April and his XO, Alexander Marcus conducted a survey of the planet Phaedus IV around 2239 . There, April witnessed a civil war between the Phaedans and saw the atrocities carried out by the Shadow. Thus, April decided to violate the Prime Directive and assist the blue Phaedans. April then took some technology and Marcus reported that April had been killed. For the next twenty years, April and the blue Phaedans fought the Shadow with supplies from Section 31 sent through the smuggler Mudd. April then discovered that the Shadow were being backed by the Klingon Empire. (TOS - Countdown to Darkness comics: "Issue 1", "Issue 2")

April and Mudd Incident Edit

Main page: Mudd Incident

Following the Gorn's attempted invasion, the Enterprise under Captain James T. Kirk was ordered by Admiral Christopher Pike to do a survey on Nibiru. However, Admiral Marcus had the Enterprise do another survey at Phaedus IV. Once there, the Enterprise detected a high frequency energy field coming from the planet. Kirk took a landing party to investigate the energy field. As they made their approach, Kirk's shuttle came under fire from the natives and was forced to crash land on the surface.

Kirk and Spock were then found by a group of Phaedans equipped with starfleet equipment and a Universal translator. Kirk asked where they got the equipment and Captain April revealed himself to Kirk. April, lying about Sulu and Hendorff's location, took Kirk and Spock into a cave protected by holographic camouflage. April revealed that he chose to stay behind in order to protect the Phaedans from the Shadows' attrocities by violating the prime directive. He also revealed that Marcus, when he was the USS Enterprise's XO, faked his death, stayed in contact with him and supplied technology to him through Section 31 and the smuggler Mudd. Spock was able to rescue Sulu and Hendorff from the Shadow and discovered that the Klingon Empire were backing the shadow with weapons.

April, using Protocol 31, was able to take control of the Enterprise. He then contacted Commander Kor and offered him the Enterprise in exchange for the governorship of Phaedus. However, Scott was able disable the protocol and enable Kirk to take the Enterprise back from April and leave Phaedus. Kirk was then ordered to leave April at the next starbase.(TOS video game: Star Trek; TOS - Countdown to Darkness comics: "Issue 1", "Issue 2", "Issue 3", "Issue 4"; TOS - After Darkness comic: "Part 1")

Marcus and Section 31's plans Edit

When Marcus became the head of Starfleet in the 2250s decade, he was dissatisfied with the Federation's response to the Klingon Empire's belligerent expansion. Believing war with the Klingons was inevitable, Marcus and a Section 31 faction sought ways to militarize Starfleet. Following the destruction of Vulcan in 2258 , the USS Vanguard discovered the SS Botany Bay, that had 73 Augment Humans from the late 20th century Earth. Marcus woke the Augments' leader, Khan Noonien Singh. Marcus then had Khan surgically altered and recruited him into Section 31 under the alias "John Harrison". At Io Facility, Khan was able to revamp the USS Vengeance's warp drive up close to Warp 10. He also refine the facility's computer system.(TOS movie & novelization: Into Darkness; TOS - Khan comics: "Issue 4", "Issue 5")

Khan then carried out a mission to wipe out Praxis. To carry out this mission, Khan invented a personal transporter unit. During his time with Section 31 and on Praxis, Khan had memory flashes and eventually completely regained them. Khan was able to convince Marcus to allow finish his modifications to the advanced long-range torpedoes in the Kelvin Memorial Archive in London. There, Khan found his crew in stasis. Khan, impersonating Marcus, was able to load his crew into the torpedoes. (TOS - Khan comics: "Issue 4", "Issue 5"; TOS movie & novelization: Into Darkness)

Khan's revenge Edit

"I had no choice but to escape alone. And when I did, I had every reason to suspect that Marcus had killed every single one of the people I hold most dear. So I responded in kind."
Khan Noonien Singh, 2259


Before leaving with his crew, Khan visited Marcus at his home in San Francisco. There, Khan revealed that he knew who he was and demanded to know how he was found. Marcus revealed how the Vanguard found him and how he surgically altered Khan's appearance. He also Khan was a test to recruit his followers into Section 31. Khan then attempted to kill Marcus, but Marcus was able to call in several Jumpships to hold him at gunpoint. Marcus also revealed that he knew where he hid his crew and threatened to eliminate them if refuse to continue working with Section 31. However, Khan escaped and believed that Marcus had made good on his threat to kill Khan's crew. Khan plotted revenge on Starfleet. He approached Section 31 officer Thomas Harewood, whose daughter Rima Harewood was terminally ill, and offered to save her life if Harewood would destroy the London's Archive. After Khan fulfilled his part of the bargain, Harewood did likewise by detonating a bomb disguised as his Starfleet Academy ring, killing himself and 41 others. In the ensuing chaos, Khan salvaged a portable transwarp beaming device from the rubble.

The bombing mandated a meeting of Starfleet's senior leadership at the Daystrom Conference Room in Starfleet Headquarters, where Marcus declared a manhunt for "Harrison". Having anticipated just such a meeting, Khan commandeered jumpship 208 and attacked, killing Christopher Pike and several other officers before he was forced to withdraw by James T. Kirk. Khan escaped via transwarp beaming to the uninhabited Ketha Province of Qo'noS, where Starfleet could not follow. (TOS - Khan comic: "Issue 5"; TOS movie & novelization: Into Darkness)

Path to war Edit

"That's what scares me: This is clearly a military operation. Is that what we are now? 'Cause I thought we were explorers."
Montgomery Scott


Following Khan's murder of Admiral Pike and his escape to Qo'noS, Kirk begged Marcus to reinstate his captaincy to the Enterprise in order to pursue Khan. Marcus, seeing a way to keep the conspiracy under wraps and to start a war with the Klingons, granted Kirk's request. He order Kirk to take the Enterprise to the edge of the Klingon Neutral Zone and kill "Harrison" with his long range torpedoes that contained his crew unbeknownst to Kirk. Marcus had the Enterprise's warp core sabotaged so that the Klingons would find the Enterprise after they launched the torpedoes.

Kirk, after reinstating Spock as his First Officer, was convinced by him to capture "Harrison" and bring him to trial in accordance to Starfleet regulations and Federation law. Kirk allowed Lieutenant/Dr. Carol "Wallace" aboard to assist him. Wallace, who was in actuality Admiral Marcus' daughter, wanted to examine the torpedoes. Despite the warp core failure, Kirk used Mudd's K'normian trading ship to land in the Ketha province while Sulu threatened to fire the torpedoes at "Harrison". However, Kirk's and his landing party ran into a Klingon patrol. Despite the patrol, Harrison eliminated the Klingons and surrendered to Kirk when Spock told him there were 72 torpedoes aboard the Enterprise, knowing that his crew were still alive.

Kirk, with his landing party and "Harrison" as his prisoner, returned to the Enterprise. Uhura contacted Starfleet but recieved no response. "Harrison", knowing that Marcus had sabotaged the Enterprise, convinced Kirk to open a torpedo and gave him the coordinates to Io Facility. While Kirk contacted Scott, he allowed Drs. Marcus and McCoy to examine the torpedo, which revealed a man in a ancient cryotube. "Harrison", revealing himself as Khan Noonien Singh, told Kirk and Spock that Marcus found him and used him to build weapons to use in a eventual war with the Klingons.(TOS movie & novelization: Into Darkness)

Battle over Luna Edit

"War is coming – and who's gonna lead us? You?! If I'm not in charge, our entire way of life is decimated!"
Alexander Marcus


Marcus, knowing that Kirk was about to uncover the conspiracy, took charge of the Vengeance and took to meet up with Enterprise. Unbeknowst to the Admiral, Scott was able to board the Vengeance after receiving the coordinates from Kirk. Upon the Vengeance's arrival, Marcus demanded that Kirk turn Khan over to him and Kirk to fire the torpedoes. When the Enterprise attempted to escape into warp, Marcus knew he needed to silence the Enterprise and it's crew.

Enroute to Earth, the Vengeance was able to overtake the Enterprise, and bring her out of warp near Luna using the Vengeance's advanced phasers. After Marcus beamed his daughter over to the Vengeance, Marcus ordered the Enterprise to be destroyed despite Kirk's pleas of mercy. However, Scott was able to shut down the Vengeance, much to Marcus' chagrin. The temporary shut down allowed Kirk and Khan to board the Vengeance. Spock also took the opportunity to contact Ambassador Spock on New Vulcan about his encounter with Khan.

Kirk and Khan were able to board the Vengeance and meet up with Scott. The three of them were able to reach the bridge, and subdue Marcus' crew. After Scott stunned Khan, Kirk demanded that Marcus step down and surrender to him instead stunning him in front of his daughter. Khan, ;pretending to be stunned subdued Scott, Kirk and Dr. Marcus. Khan then crushed Admiral Marcus' skull and killed him. Khan then demanded Spock to give him his crew or he would kill Kirk. Spock, knowing that Khan would betray due to Ambassador Spock's warning, gave Khan his torpedoes. After beaming Kirk, Scott and Marcus back to the Enterprise, Khan fired the Vengeance's phaser at the Enterprise. However, Spock had Dr. McCoy removed Khan's crew from the torpedoes and detonated them in the Vengeance's cargo bay.

Both the Enterprise and Vengeance were critically damaged and caught in Earth's gravity falling towards the surface. Kirk was able to save the Enterprise from crashing by reactivating the warp core. However, he suffered radiation poisoning and believed to be dead. Khan, believing his crew had been killed, attempted to pilot the Vengeance into Starfleet Headquarters. However, it crashed into Alcatraz and crashlanded into San Francisco killing many civilians. Khan attempted to escape, but was pursued by Spock, who wanted to kill him. However, Uhura told Spock to spare him knowing Khan's blood could save Kirk's life. Spock was able to incapacitate Khan.(TOS movie & novelization: Into Darkness)

Aftermath Edit

"When Christopher Pike first gave me his ship, he had me recite the Captain's Oath, words I didn't appreciate at the time. Now I see them as a call for us to remember who we once were, and who we must be again."
James T. Kirk


Dr. McCoy was able to perform a blood transfusion that save Kirk's life. Khan was then brought to trial where he revealed his origins, his Section 31 service and betrayal. He was then placed back with his crew in stasis. Starfleet also began a comprehensive effort to remove all trace elements of Section 31 operated by Marcus. April was sent to Starfleet Security in San Francisco and revealed to Kirk that his plan was to distract the Klingons while Marcus would lead a frontal assault against the Klingon Empire.

A year later, Kirk spoke at a memorial dedicated to the victims of the conspiracy due to Marcus' and Khan's actions. He reminded the attendees of Starfleet's true mission of exploring the galaxy. Following the service, Kirk led the Enterprise on it's first five-year mission. Starfleet would continue being explorers, not a military organization. (TOS - Khan comics: "Issue 1", "Issue 2", "Issue 3", "Issue 4", "Issue 5"; TOS movie & novelization: Into Darkness; TOS - After Darkness comic: "Part 1"; TOS movie: Beyond)

Despite Starfleet's efforts, Section 31 continued with operations against both the Klingons and the Romulan Empire. They provided the Romulan warbirds under Commander L'Nar with weaponry based on the Vengeance's systems. (TOS - Khan comic: "Issue 1"TOS - After Darkness comic: "Part 1"; TOS - The Khitomer Conflict comic: "Part 1")

External linkEdit

Militarization conspiracy article at Memory Alpha, the wiki for canon Star Trek.

Community content is available under CC-BY-SA unless otherwise noted.