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"If you've got something to say...say it. Tomorrow's too late."
- - Alexander Marcus, 2259
In 2259, Pike convinced Marcus to alter the punishment for his protégé Captain James T. Kirk, who was being sent back to Starfleet Academy for breaking the Prime Directive. Kirk would instead be demoted to Pike's first officer on the USS Enterprise.
Following the destruction of Vulcan in 2258, Marcus began seeking ways to militarize and better defend the Federation. In particular, he foresaw war with the Klingon Empire as inevitable. Section 31 discovered the SS Botany Bay, and Marcus revived Khan Noonien Singh, recruiting him under the name John Harrison to design weapons and ships.
However, Khan resented Marcus's control over him and the use of his fellow surviving Augments as hostages, and attempted to smuggle them out in the experimental photon torpedoes he created. He was discovered, and Khan was forced to flee alone, beginning a one-man war on the Federation as he presumed Marcus killed his crew.
On stardate 2259.55, Khan coerced Section 31 agent Thomas Harewood into bombing the Kelvin Memorial Archive in London. Marcus received a message from Harewood before he died explaining Harrison threatened him, and the admiral declared a manhunt at a summit in Starfleet Headquarters. Khan, aware protocol dictated a summit like this one, appeared in an attack vehicle and opened fire. Khan was forced to flee however, and Marcus survived, though Pike was killed.
The following morning, Kirk reported Harrison had used the confiscated transwarp beaming formula to escape to Qo'noS. Marcus ordered Kirk to pinpoint and execute Harrison with the 72 experimental photon torpedoes he had designed. Spock deemed Marcus's orders to execute Harrison without trial immoral, and Montgomery Scott found it suspicious that he was not allowed to examine the torpedoes, making Kirk decide to arrest Harrison instead.
Once Kirk discovered the truth from Khan, Marcus showed up in the USS Vengeance — a warship designed by Khan — demanding Kirk hand him over. When Kirk attempted to flee to Earth to put Khan on trial and expose Marcus, the Vengeance caught up and crippled the flagship. Marcus's daughter Carol revealed she was on the Enterprise, but the admiral simply had her beamed up and prepared to wipe out all evidence of his scheme. Fortunately, Scotty had boarded the Vengeance at coordinates given by Khan and deactivated its weapons. Khan and Kirk donned thruster suits and flew over to the ship to commandeer the bridge. Kirk confronted Marcus over his betrayal of everything the Federation stood for, but Khan ended the lesson by knocking him aside and caving in Marcus's skull: the sight prompted screams of horror from Carol.
"By now, some of you have heard what happened in London. The target was a Starfleet Data Archive, now it's a damn hole in the ground, 42 men and women are dead. One hour ago, I received a message from a Starfleet officer who confessed to carrying out this attack, that he was being forced to do it by this man: Commander John Harrison. He's one of our own, and he's the man responsible for this act of savagery. For reasons unknown, John Harrison has just declared a one-man war against Starfleet, and under no circumstances are we to allow this man to escape Federation space. You here tonight represent the senior command of all the vessels in the region, and in the name of those we lost, you will run this bastard down. This is a manhunt, pure and simple, so let's get to work."
- - Alexander Marcus explaining the London bombing
"Well, shit! You talked to him."
- - Marcus, upon realizing that James T. Kirk knows John Harrison's true identity
"That's a hell of an apology, son. But if it's any comfort, I was never gonna spare your crew. Fire."
- - Marcus, after Kirk offers himself in return for the Enterprise's safety
"War is coming, and who's gonna lead us? You?? If I'm not in charge, our entire way of life is decimated! So, you want me off this ship? You better kill me."
- - Marcus to Kirk, with the latter trying to arrest him at gunpoint
Alex Marcus was played by Peter Weller, who also played John Frederick Paxton in Star Trek: Enterprise. The character was described by producers Damon Lindelof and Bryan Burk as being their attempt to incorporate a trope of Hong Kong cinema into the film, where the hero (Kirk) and villain (Khan) must temporarily set aside their differences.
Weller compared Marcus to Curtis LeMay, a proponent of nuclear war. LeMay "had eighteen nukes stored on his own that he didn’t tell the NSC or President Kennedy about — because he didn’t deem them knowledgeable enough about war. That is unbelievable arrogance! So, Admiral Marcus is basically like LeMay." However, he opined that Marcus actually has a conscience because he wants to undo his mistake, but what "makes him bad, from a moralistic view, is that he's willing to sacrifice Kirk and the Enterprise to put this thing back in its shell.  The Washington Examiner found parallels between Marcus and Dick Cheney, to which Simon Pegg responded "Absolutely, he's definitely a Republican." 
The IDW comic series Star Trek: Countdown to Darkness, set in the alternate reality, reveals that Alexander Marcus at Memory Beta, the wiki for licensed Star Trek works was the first officer of a previous starship Enterprise at Memory Beta, the wiki for licensed Star Trek works which existed subsequent to the Enterprise (NX-01), but prior to the new USS Enterprise.