This is a Gundam Seed Destiny/ StarTrek Crossover with a tiny bit of Robotech
Events happen after Star Trek Nemesis and Voyager return from the Delta Quadrant
Disclaimer as always, I don't own them and if did, then I'd be a rich Man.
Prologue
April
3, 73 OF THE COSMIC ERA
The Second Bloody Valentine War
Revelations of Chairman Gilbert Dullindal Destiny Plan, the total Annihilation of the main bulk of the Earth Alliance Fleet and Arzachel Lunar Base by the captured Requiem two days ago have reveal the true intention of Chairman Dullindal. What remains of the Alliance fleet have regrouped and joined up with Terminal under Lacus Clyne command alongside with their Orb ally.
They prepare for the final conflict that will decide the fate of the world.
Somewhere in Bozeman, Montana in North America
An old US Air Force Missile Silo, is an Earth Alliance Jet Propulsion research Laboratory where they study the possibility of faster than light travel, though not much of a research center but more of a refugee camp for those that survived the 'Break the World' operation by Coordinator terrorist.
Inside one of the missile silo, houses a single decommissioned Titan II nuclear missile, left behind without the nuclear warhead. Now it is the launch vehicle for the first their first spaceship.
Zefram Cochrane and his team of engineers are doing some last minute calculation check and equipment test before they launch as a battle is being wage in space. Cochrane and his team is working on an old late 20th Century computers as most of their more modern equipment were acquisition by the Earth Alliance as the War escalated and after the Loss of Heaven's Base, their only remaining super computer were taken and have been ordered to shut down their experiment.
They didn't shut down or left, instead they continued to finish their studies without EA support or equipment. They made due on what they can salvage from warehouses and junkyard of obsolete equipment and technology in order to finish their work. It was slow going but they persevere, and the 'Phoenix' is ready to fly.
"Yo Z!" Lily Sloane called Cochrane by his nickname 'Z' for Zefram
"We gonna have to postpone the launch, there's a battle happening up there in L4"
"There's always a battle happening up there" he said and sigh in frustration as there were too many launch delay and he has had it.
"Dammit!" he cursed in irritance
"No we are launching" he announce lily protested
"Z we can't launch up there, you are gonna get shot at by either Earth Alliance or Zaft for god sakes"
"I'll take that chance," he replied "For once, just once I want to finish something that I have started!" coming out of silo shouting and then look up at the night sky
"We will go as scheduled, and our launch window is far enough from them, and they will be too busy fighting each other to even care what were doing" he look back to Lily and said "Once were finished, then we will know that 3 years of our life working on this thing is worth it or not"
In Space
Zaft's Mobile Fortress Messiah is preparing to fire a second shot of their Neo Genesis at Lacus Clyne ship the Eternal and the Allied Fleet who came to stop Zaft from firing the Requiem Cannon at Orb, the last nation that stands against his way.
The Orb Fleet quickly reorganized for a second assault with their Mobile Suit forces playing interference.
Eager to destroy the ones that stand in his way, Dullindal ordered Neo-Genesis to fire without fully charging. The beam fire destroyed several ships including those belongs to Zaft but missed Lacus ship the Eternal, the Archangel.
The Genesis beam continued its path of destruction for several hundred thousand kilometers. But in its path is a huge Mount Everest size black rock phasing in and out of the spacetime continuum unnoticed by everyone is in its path. The beam of Gamma Radiation struck it in full force and caused a chain reaction that unleash a temporal wake that washes all across Earthspace, and as its energy washes everything in space, every colony, satellites, debris fields, ships and mobile suits started to disappear except for the ones behind the moon and earth as if it was shielding them from the incoming tide.
It was one of the most strangest phenomenon ever. Everything in its wake has disappeared leaving the Earth and some of the people on the moon and unaffected colonies question what has just happen.
Even the Requiem went silent as the cannon collapse on itself. Whatever the Neo-Genesis has struck ended the battle so dramatically.
Immediately a ceasefire was called on both Zaft and Earth Alliance forces and remnants of Orb that remains, as they were too stunned of what had just happened.
All colonies from L1 to L6 are gone. The Plants colonies, neutral nations and a few Earth Alliance colonies and outpost have disappeared without a trace, and an eerie silence surrounds the Earth.
48
Hours later
April 5, 73 of the Cosmic Era
After one day delay (By outside interfernce), The 'Phoenix' launches from its missile silo to begin the first test flight. Manned by Zefram Cochrane himself he flew the Phoenix in an area of space that was battlefield a day ago, there are no debris, no satellites or colonies, just space.
Ignoring of what has happen yesterday he focused on the experiment and flew the Phoenix pass the speed of light. Unbeknownst to him an alien ship that was passing by on a survey mission spotted the warp trail of the Phoenix and decided to investigate.
It was on this day that a new page in man's history is turned and a new one is about to begin.