Disclaimer: I don't own Star Trek or Babylon 5, even though I wish I did.
AN: There won't just be elements of the show, but elements of the Star Trek: Armada II game in this story. There may also be some fudging of dates and the timeline.In this timeline, Voyager returned to the Alpha Quad with the Ablative Armour and such before the Cardi's and Dominion were able to kill off the Maquis. Also, there will be a fraction of the population from the Star Trek universe who have telepathic powers (like the Babylon 5 universe)
AN2: I did a bit a rewrite here. Changed some names and cleared some things up.
A fleet of what appeared to be Federation ships orbited a moon on the inside of the Badlands. This was the last stop on their voyage, before they left behind Federation space forever. The fleet belonged to The Maquis, who could no longer take the Federation policies criminalizing them. The Cardassians had also joined with The Dominion, who had started killing all the Maquis down to the last man, woman and child.
There were around a hundred thousand people crammed onto thirteen ships. There were no quarters, with every spare space taken up by bunks. People were even sleeping in the jefferies tubes. The only places without multi-level beds in there were the Bridge, Engineering and some cargo bays. Each ship had only a name, without the 'USS' or reg number of Federation ships. The fleet was made up of:
One Sovereign Class ship called The Avatar, with a Contruction Ship called The Muir in her belly.
One Galaxy Class ship called Scimitar.
One Nebula Class ship called Tribal.
One Interpid Class ship called Hawkins.
One Akira Class ship called Merlin.
One Ageian Class ship called Leviathan.
One Colony Ship called the A'tuin.
Two Sabre Class ships called Juno and Jupiter.
Two Venture Class ships (with cloaking devices), called the Atlas and The Endurance.
Three Defiant Class ships called Maya, Aeyr and Sarapis.
All ships had been installed with Ablative Armour that was bought back to the Alpha Quadrent by Voyager.
A contruction ship and the Delta Flyer had been comandeered by the returning Commander Chakotai with Tom Paris, Be'lanna Torres, their daughter and all the former Maquis from Voyager. Upon their return to the Maquis, they learned that the Dominion were moving to destroy them all.
The Avatar was the flag of their fleet, which was commanded by Chakotai, with Tom Paris commanding The Scimitar with his wife.
They found a dilithium and metal rich moon within the badlands, and were able to build their fleet within a month, then quickly collected all the people left on the Maquis worlds, before coming to their last base.
They collected the last of the supplies they had stockpiled, items that can be broken down for replicators, metals and dilithium for repairs and construction. Seeds and samples that could be used for the cloning of animals.
When they left the moon base, they set out of the badlands, and set course away from Federation and Cardassian space, in the direction that would take them to the Gamma Quadrent in a decade or two, though they didn't intend to spend that long travelling.
However, two weeks into the journey, they came across what seemed to be a wormhole. They studied it for a long time, finding it led to an area of space with no Federation signals, or known species within sensor range. Even better, there was an 'M Class' planet with several moons, rich in Dilithium, metals, and edible plants and animals within a short distance of the exit point.
The commanders and civilian council met and quickly chose to travel through the wormhole and make a new home on the planet.
In short order they began to colonize the planet with farms, mines and they were able to build a city very quickly, building enough housing for all the people on the ships. Pulse cannons and torpedo turrets were placed in orbit, with mining stations around the moons as well.
Within a month, the planet was heavily fortified, and there was even a ship-yard being built.
It was decided to send the Atlas and Endurence out to search the surrounding area of space. When they came back, it was with disturbing news. They were actually relatively close to Earth – However, it wasn't their Earth.. and this Earth's government had just started bombing Mars and declared Marshall Law. Word was also brought back of a space station that had just broken away from that Government called Babylon 5. Feeling that this station may be similar to their Marquis, with EarthGov being list the worst of the Federation and the Cardassians rolled up together, they decided to make contact with the breakaway station. So The Avatar, Scimitar, Maya, Aeyr, Sarapis, Hawkins and Merlin left the orbit of their planet that was now called Gallifrey, and set course for the Station.