After the Master's defeat, Marcus wandered aimlessly, looking for fellow super mutants. In the year 2185, at high noon, he encountered a Brotherhood of Steel Paladin in power armor named Jacob, who had pledged himself to the extermination of all mutants. They fought for days with guns and fists, but eventually gave up, each unable to get an advantage over the other. Eventually, they realized the pointlessness of their fight, and broke down in joined laughter, beginning a strong friendship between them. The two started traveling together, arguing over the Unity and Brotherhood doctrine and whether or not the Master could truly neurolink his biology into the Cathedral computer network. As they wandered through the wastes, they attracted a following of other refugees from the war, who believed that Marcus's strength and Jacob's power armor gave them the closest thing available to safety. In Fall of the same year, Marcus and Jacob, along with the trail of ghouls, humans, and super mutants, founded the community of Broken Hills.
After the Chosen One helped him expose an anti-mutant conspiracy in Broken Hills, Marcus joined him on his quest to find the Garden of Eden Creation Kit, and eventually to save the people of Arroyo from the Enclave. When the group's task was complete, Marcus returned to Broken Hills and watched over the town until the uranium mine ran dry and the place, no longer having an economic foundation, was deserted by its inhabitants.
As his position as sheriff of Broken Hills had outlived itself, Marcus, inspired by the example set by the Chosen One, started wandering east, across the great mountains, in search of other super mutants. He never found out what happened to his tribal friend from Arroyo, but he had a feeling that he did good in the end.
Marcus eventually reached the Mojave Wasteland, where he founded a community for super mutants atop Black Mountain. This fell apart when Tabitha, an insane nightkin, rallied the less intelligent Enclave-created mutants against Marcus and forced him and his supporters out of the area. By 2281, Marcus had found Mount Charleston, where he founded yet another safe haven for mutants, naming it Jacobstown in honor of his old friend. At Jacobstown Marcus helps and protects schizophrenic nightkin, and hopes to find a cure with the help of former Enclave scientist Doctor Henry. Marcus will also greet the Courier and warn him about the nightkin within Jacobstown when the Courier enters Jacobstown for the first time.
Marcus can join the Chosen One's party after the mine purifier has been fixed. He is skilled with big guns and large energy weapons. However, sometimes his use of burst weapons are as devastating to the party as to enemies. Also, as with all other super mutants (barring those in Fallout Tactics) he is incapable of wearing armor, which leaves him somewhat vulnerable. However, Marcus does have innate armor statistics that increase as he gains in abilities, thus mitigating his inability to equip armour. At his highest level, he has the equivalent of a suit of combat armor. Also, the ammunition for his big guns can be hard to come by and expensive to purchase (this can be dealt with, by arming Marcus with a turbo plasma rifle which, while still decent in terms of damage, has a much lower maintenance cost).
Having Marcus in your party will generally cause you to be denied entry into the inner sections of Vault City (though not the southern courtyard), so you will have to leave him outside and pick him up on the way out. Becoming Captain of the Guard allows you to get Marcus past the guards, but if First CitizenLynette sees you with him, you will be kicked out of the city for good.
Should you have both Lenny and Marcus in your party, Marcus will occasionally say things like "Nice to have another evolved human in the group, Lenny", "Hey Lenny! Ever been to Broken Hills?" and "Lenny! Let's get somethin' to drink!", indicating that the two have known each other in the past, or simply that Marcus considers their shared mutant status confers on them a brotherhood of sorts.
Taking him to Troy in Vault City to be healed will get him purged of the various bullets embedded in his thick skin, which Troy will then give to you. You get 20 7.62mm, 40 .44 magnum JHP, 40 .44 magnum FMJ, 50 5mm JHP, 10 .45 caliber, 24 10mm JHP, 50 .223 FMJ, and 20 9mm ball. He has been shot by a lot of people. Note that this can only be done if you are the Captain of the Guard, otherwise Troy will attack you for bringing a mutant into the city.
While Marcus says that he is no longer sterile, Chris Avellone, who wrote that dialogue, confirmed that Marcus was only joking and that super mutants remain entirely sterile.
During combat, if Marcus is hit by an enemy weapon, he may occasionally cry out, "I am NOT a merry Mutant!" This is a reference to Michael Dorn's role as Worf on Star Trek: The Next Generation, specifically the episode "Qpid", in which Worf protested to being given the role of a "merry man" in Q's Robin Hood recreation.
Marcus might say when unarmed and attacking: "one fist, two fist, red fist, blue fist". This is a reference to the Dr. Seuss book One Fish, Two Fish, Red Fish, Blue Fish.