Mobile Suit Babylon: As the Universal Century dragged on, it seemed as if mankind was fated to fight for centuries to come. But as traverse come from other systems, the conflict between those in space and those on Earth seems trivial.
Crossover between B5 and Mobile Suit Gundam with the Centauri contact happening some point in the early years of the 2nd century UC or final years of the 1st.
Mass Effect: The Anhur Rebellion: In the middle of the 2170s, the world of Anhur saw one of the greatest violations of sapient rights in modern human history. Its people fought against the abuses and won. This is the story of the Anhur Rebellion.
A documentary style story of the events of the Anhur Rebellion, an interesting background event that takes place in the Amun System.
Those Left Behind: A patrol ship far from home, a campground far from civilization, a dome deep beneath the waves, a mining colony deep in space. These and a thousand other holdouts who didn't get a dying leader, destined to die out and be forgotten by the will of prophecy. But the enemy of fate is man's will, and the night will not take them.
People survive in relatively large numbers across the colonies, surviving and, much later, mostly meeting up.
Either a crossover or a future Earth comes in later, or independently in the beginning at the edges of colonial space. They eventually meet the survivors and begin to help them, maybe even bringing them away from the colonies. perhaps resettling them on New Caprica under that or another name (New Picon maybe).
Eventual contact with the fleet, creating a double whammy of meeting humans from Earth that are very different from the colonials with motivate levels of genetic engineering, notable cybernetic enhancements, different religions if any at all, and neural cybernetic connections like the cylons, alongside a large number of colonials who don't want to be under the fleet's government.
Perhaps the Earth humans are interested in Cylon resurrection (eternal life), which causes problems with the fleet colonials (I can already see the conversation with Roslin about becoming more like the Cylons "you are making yourself less human" "âand? It's only a form for our minds, doesn't really matter if it's the same thing we were born with, it's replaceable.")
Earth is generally more technologically advanced than the colonials, but the lack of major wars has led to a relatively small military and limited developments in weapons tech (advanced kinetics and missiles, but no energy weapons), making the Battlestar and Basestars notable threats through each being vastly larger than any Earth warship in service.
The Marked of Man: One day, the galaxy was swarmed by two massive armies of a race never before seen. But they did not ravage the galaxy, instead they defended the innocent, helped the weak, and tried to make the galaxy a better place. When asked why, they would say shame, and redemption.
Humanity spent longer in space than in cannon. During that time it split into two groups that began to fight one another, doing lots of war crimes and genocide.
One day, something is revealed that leads to the leaders of both sides being disposed and the war ending (thinking either a 1984 style of keeping the wars on just to stay in power, Reaper influence, or something else), but the militaries are a problem. The people don't want them to stay due to their many, many crimes (population suppression, killings, and other levels of crime that would make the nazies blush), and the military deals shame for the countless horrors they inflicted on others while fighting for a cause that proved to be little more than a lie.
This leads to what was basically banishment, millions of military personnel and those who chose to go with them were given the ability to sustain themselves near indefinitely, pointed at the depths of space, and told to never return.
The exodus continued until the forces made it to the known galaxy, where they saw a chance to gain some form of atonement by helping the people of the galaxy, supporting colonies, hunting pirate, killing slavers, ect. This, of course, ruffles some feathers, but they do it anyways.
They start to take on volunteers from the local populations for pay as they grow and/or lose numbers (some groups continue population growth, but others don't wish to increase their human numbers, but of a social divide that can be used for conflict in the story, those who wish to continue humanity In the galaxy and those who wish to end their lines with those who earned their exodus).
Humans have the ability to download after death (like Cylons), and are biologically immortal due to the enhancements given to them during the war. However it is possible for them to die if they are out of resurrection range or their mind is destroyed while waiting to be given a new body.
Humanity remains relatively secretive of their origins, telling nearly mother to outsiders and only telling the most trusted aliens among their ranks.
The military structures of the humans has mostly fallen (though rank is still respected), with them mostly operating in independent groups on their own, though commonly cooperating when needed.
Story follows a Quarian who went on their pilgrimage and ended up joining a human group.
The Fantastic Fight After Death of Preston J. Cole: When he saw the writing on the wall, the inevitability of defeat, he did the only logical thing; he ran, taking those he could and running far into deep space after winning one last victory. Now a new enemy is at the gates, and they will deal the wrath of the greatest admiral of mankind.
A Halo Battlestar Galactica crossover where Preston J. Cole, the Insurrectionists, and those civilians they could same, escaped from human space to what would have been known as New Caprica, now known as New Harvest in honor of the first world destroyed by the Covenant. A few decades later, the colonials arrive with the Cylons on their tail.
For power scaling; the Halo ships are powerful, a MAC ripping through anything from BSG like a hot knife through butter and a grand missile swarm ripping anything not protected by a holy wall of flack to pieces, but the few warships they have are either early war upgraded or pre war standard vessels, meaning they aren't exactly soloing an entire fleet, and all the warships besides the Everest are Frigate size or smaller, and quantity (of mass) has a quality of its own. Alongside that, the Slipspace Drives of New Harvests ships are very slow compared to the colonial jump drives, with even the fastest not breaking 5 light years per day compared to the maximum of 15 in one jump for the colonials, though most jumps are at 5 light years or less and are only taken every 12 hours to avoid damage to the engines.
Colony's population is high hundreds of thousands to low millions, higher population than the colonials, but not by so much they are only a footnote, especially after some more people are rescued from the 12 colonies.
The reaction of the colonials ti AI will be fun, and the Halo human and AI response when they look into a Centurion's code and find it is basically a Smart AI that went through the equivalent of RvB Alpha's treatment (copy, copy, copy) and then were enslaved by both their own creators, and later creation, will be funny. I'm thinking of a Centurion enclave existing on New Harvest, both due to my general liking of the Centurions and the fun reaction of the colonials.
The UNSC will be contacted later in the fic (cannon divergent as of Halo 3 or 4 and a decade or two after the war).