This isn't really gonna be a narrative explanation, but rather more of a "following along with the slides" sort of deal. Assume a Good Karma Wild Card ending. The Courier sided with Mister House, following that "questline" until he met with Ulysses at the Divide. Realizing the nature of the banner he was carrying - no better than the Big Empty brains - he turned against House and took control himself. Some of this doesn't really follow the gameplay, but I've edited it to "fit the narrative" story. Some of it diverges significantly, but I think they fit the tone in any case.
Final Victory: The Courier, with the help of the Securitron Army and Yes Man, throw out the Legion and the NCR from the Mojave and establish an independent state in the region. General Oliver goes home, unscathed but with a dead career, and Lanius retreats to fight another day.
Black Mountain: The Courier fought his way to the summit while serving the Brotherhood of Steel. Pinned into one of the buildings, he desperately set off repairing the Mister Handy lying in storage. As he kicked out the door, ready to go down guns-blazing, he was confronted by Tabitha, the head mutant. She quickly changed, setting off with the Mister Handy. Stories reached the Mojave of the pairs travels into Arizona and beyond - but few believed them.
Raul Tejada: The Courier set Raul free while stumbling through the ruins of the Black Mountain, taking him along with the rest of his entourage. Telling his stories of the past to the Courier, he encouraged the Mexican Ghoul to take up his guns once more - to fight for freedom once more. Shortly after the fighting with the Courier at the Hoover Dam ended, he set off eastward - becoming something of a folk-myth of the tribals of Arizona and beyond, hunting down Cult of Mars Legion remnants and tribal slavers.
Boomers: With their B-29 flying high, the Boomers set about strengthening their position in Nellis, repairing some of the fighters lying in the hangars. In the immediate aftermath of the Declaration of Independence, Vegas fell into anarchy - but Nellis remained. As the chaos calmed, the Boomers began to trade more openly with the Courier's State - though never fully giving up their hard-fought independence.
Brotherhood of Steel: The Mojave Chapter of the Brotherhood of Steel was destroyed in a cataclysmic explosion ordered by Mister House. The survivors of the Chapter fled into the Wasteland, heading back to Lost Hills in hopes that the Western Elders would take the back - or heading East, spurned on by rumors of chapters in the Midwest and in Washington DC.
Veronica Santangelo: Encouraged by the Courier to join the Followers of the Apocalypse, she left his retinue to study under the service of Julie Farkas at the Old Mormon Fort. She heard the rumors of the destruction of the Hidden Valley and confronted the Courier. She could understand his motives, as Mister House ordered their destruction, - but she could never forgive them. And when she found out that the Courier turned against Mister House in the end, she left Vegas entirely, in disgust with a man she had once called a friend. She left with a contingent of the Followers traveling with the Great Khans up to Montana, disappearing into the mists as Papa Khan forged the Great Khaganate of the North.
Fiends: While working with the NCR Army, the Courier and his entourage - alongside a contingent from 1st Recon - killed the four major players of the Fiend gangs. Without the clear leadership, they disintegrated and splintered into the Wasteland. Some of the minor leaders attempted a power play in the anarchic months following Hoover Dam, but were rapidly repulsed by the militias of Outer Vegas.
Followers of the Apocalypse: In the aftermath of the Second Battle of the Hoover Dam, and in the Anarchy that followed, the Followers were overwhelmed with patients. No matter how much the Courier tried to aid or assist them, it was never enough - but they appreciated the sentiment nonetheless. As the chaos subsided, the Followers established themselves in all the Boroughs of Vegas and in each of the surrounding towns of the Mojave Wasteland - the Courier acting as a benevolent patron of their arts. They were granted, as a show of gratitude by the Courier, administration of the HELIOS One Station, ensuring that power flowed freely to all in the Mojave.
Arcade Gannon: The Courier, while uniting the Enclave Remnants, encouraged Arcade to take his own path - and encouraged him to remain in Freeside with the Followers. Arcade quickly became one of the more prominent members of the Followers, establishing a name for himself as he set up outposts in each of the towns and communities in the Mojave. Five years after the Battle of Hoover Dam, growing dissatisfied with life in Vegas and with the Followers, he headed back to California, establishing a practice in the Boneyard.
Goodsprings: The Courier sided with the Town, forming the militia and driving the Powder Gangers away. The town flourishes as a way-stop along the 15, attracting traders and even tourists looking to see where the Courier rose from the dead. They are exempt from taxes from the Free State, a token of respect from the Courier for the town that saved his life.
Rose of Sharon Cassidy: The Courier and Cass teamed up in a showdown of the ages, that sent ripples flying back to the NCR. They dispensed with the Van Graffs and the Crimson Caravan with frontier justice - becoming a symbol of the Courier's State to many of the Californians - although quietly most in the NCR were glad to see the two titans of the industry shrivel and shake. She was surprised to see that the Courier had really, truly, actually done it. The ingenious bastard. Three armies crushed in the blink of an eye. She remained at the Courier's side, never once making the mistake of underestimating him.
Great Khans: The Courier exposed the nature of the "alliance" the Khans were negotiating with the Legion. He encouraged Papa Khan to lead his tribe from Red Rock Canyon up towards the North, to forge his tribe's true greatness. Taking these words to heart, Papa led the Khans to Montana, and with the help of the Followers of the Apocalypse, they forged the Great Khaganate, a mighty empire, out of the plains there.
Jacobstown: Helped by the Courier, Doctor Henry developed a cure to Nightkin Schizophrenia, and it became a haven in the wastes for Super Mutants seeking a place to be free and to live. They were given patronage by the Courier, who acknowledged their right to exist and secured caravans that would travel up Mount Charleston to trade with the town.
Lily Bowen: The Courier encouraged the grandmotherly Super Mutant to go on full dosage for her medicine. Her memory of her long-lost grandchildren soon faded from her mind, and she spent the rest of her life tending to the Bighorners at Jacobstown.
The Kings: The Courier eased tensions between the NCR Refugees and the Kings, ensuring that the peace in Freeside was kept even during the anarchic months after the Battle. The Kings soon became one of the more prominent gangs of Vegas, holding considerable sway over North Vegas and Freeside. The King takes some pride in the fact that the Leader of the Free State is an honorary member of the gang, and indeed, a perfect example of the Every-Man-a-King philosophy.
Rex: The Courier placed the brain of Old Lady Gibson's dog Rey into Rex's body. The memories soon settled nicely, the dog becoming a faithful companion of the Courier. Soon, the robot-dog found itself over at the Big Empty, where he and Roxie set about creating a litter of cyberdogs.
The Misfits: Encouraged by the Courier to put aside their differences and work together as one, the Misfits fought with distinction during the Legion attack at Camp Golf, dying to hold back the South Palisade from a cohort of Legionaries. They were posthumously decorated by the NCR for their valor.
Novac: The Courier faithfully assists the REPCONN Ghouls in their journey to Space. During the Battle for Hoover Dam, the Courier sent Boone back to Novac to hold the line. They barely pushed back the Legion from the town, but were thankfully aided in the rebuilding by the REPCONN Ghouls, paying a debt of gratitude to the Courier and those he called his friends.
Craig Boone: Boone, encouraged by the Courier to let the regrets and the trauma of Bitter Springs behind, hemmed and hawwed of going back to the NCR to rejoin his unit, or going off to Arizona to hunt down the Legionaries. Instead, he remained in Novac - the one town he said he wouldn't go back to. He couldn't bring himself to leave Vegas, or the Mojave, but couldn't bear to enter the city where he met his wife.
NCRCF Powder Gangers: The Courier aided the NCR Army in taking out the prison, blowing a hole in the walls and pouring in - much to the Powder Gangers' surprise. In the chaos, Eddie was shot dead along with the rest of the NCRCF Ganger leadership. Sheriff Meyers helped the Courier and the NCR Army take out the Gangers, and earned himself a pardon. As for the rest of the Powder Gangers, they fanned out into the Wasteland, most putting their old lives behind them.
Vault 19 Powder Gangers: Encouraged by the Courier, they aligned themselves with the Great Khans and petitioned to join them on their trek towards Montana. Most made it through the initiation, and headed out with the tribe up North. The ones who didn't make it filtered into Vegas, fading into obscurity.
Primm: The Courier cleared out the town from the Powder Gangers and appointed ex-con Jim Meyers as Sheriff of Primm. Since the Sheriff aided the NCR and the Courier in taking down the rest of the Powder Gangers, they gave him a pardon and he took over Primm. He leads the town firmly, with frontier justice being the rule of law.
ED-E: His logs cleared, the eyebot remained a faithful companion of the Courier - aided by upgrades installed by the Followers and also the ones found on his counterpart in the Divide. The information recovered from ED-E aided the Followers in the operation of the HELIOS One Station, and in constructing new solar power stations throughout the Wastelands.
NCR Rangers & Chief Hanlon: Chief Hanlon's record remained unbelmished, the Courier's discovery of his indiscretions remaining a secret between them - and all the paperwork lost in the chaos of the Withdrawal in any case. The Rangers distinguished themselves in the Battle of Hoover Dam, and evacuated back to Mojave Outpost under the Chief's guidance. The Rangers returned to their roots, patrolling the stretches of highway leading to the North to Ogden, Seattle, and beyond - no longer acting as shock troopers for the Army. The Chief became a Senator for Redding, a quiet ally of the Courier in the NCR Congress.
Remnants: After their bold arrival at Hoover Dam, the Remnants disappeared as quickly as they came. Legends of their power spread throughout the southwest, a reminder of why people once feared the sight of vertibirds in the sky.
Dead Money: The Courier melded the two personalities of Dog/God into one entity, killed Dean, encouraged Christine to let go of her anger and her desire for revenge, and locked Elijah in the Sierra Madre Vault. No, he did not take any gold bars (he wasn't metagaming.)
Honest Hearts: The Courier encourages the Dead Horses and the Sorrows to fight the White Legs, and tells Joshua Graham to spare Salt-Upon Wounds. He tells Waking-Cloud of her husband's death, and encourages Follows-Chalk to remain with his tribe.
Old World Blues: Full completetionist as far as the Sink goes, fully installing all of the Personality Modules and running all of the X-[number] tests on the equipment. Cyberdogs policing the Wasteland for the benefit of settlers, the REPCONN Headquarters at Henderson being turned into an X-13 Facility, all of that. The Think Tank and Mobius remain alive, contained in the Big Empty.
Lonesome Road: Ulysses remains alive, the Couriers unite to fight against the hordes of Marked Men in the silo as ED-E shuts down the launch sequence. The Courier takes Ulysses' lessons to heart, and returns to the Mojave to kill Mister House and begin the Second Battle of Hoover Dam.