The EPF was founded by President Ulysses Grant to protect Earth against alien invasion. For nearly two centuries, led by Bishop, the EPF captured aliens, such as the Roswell Greys, collected their technologies and have remained a secret except to the US President and bureaucrats.
During the Triceraton invasion, the EPF allied themselves with the Federation to find Professor Honeycutt, who had conveniently came back to Earth after the invasion, in exchange for Earth's protection from invasions.
Having observed Oroku Saki, the "savior" of New York City, repair the city, which was a cover for salvaging remaining Triceraton tech, Bishop captured his daughter, Karai to force Saki to hand over the goods. But he sends Hun instead and with the unknowing assistance of the Ninja Turtles, freed Karai.
Bishop authorized a city-wide dispersal of sonic devices that irritate rats and crocodiles on a sensitive level, to draw Splinter out. Once Splinter was captured, Bishop revealed to him that he intended to use his DNA to advance the acceleration of his super soldiers to protect Earth—possibly made from his DNA. Also, he unveiled the Slayer, his prototype hunter, a cyborg resembling him. But the Turtles and Honeycutt managed to flood the base and Bishop fled as his Slayer was washed away in a tank.
On the night of Saki's good-bye party, the EPF is prepared to storm his mansion and take any technology they can find. With the help of Dr. Baxter Stockman, they bypass security and discover Saki having built a giant spaceship to leave Earth. They damage the track controls to prevent it from leaving via remote launch pad, so Saki launches the ship through the alternative door. Trying to take down the ship, the EPF launches numerous missiles to destroy it. They thought it destroyed and Stockman worked for the EPF.
Due to the crashing at the party and lack of alien attacks and numerous "screw-ups,", the President was threaten the EPF was at risk of being shut down. Worse, the Purple Dragons hijacked a shipment of weapons, including a mutated man named Finn, who Bishop was his best man, as well as a test subject only known as T-9814. Bishop tried to go to any cost to retrieve the mutant as he makes his way to his home, but loses the subject.
With this further failure, the bureaucrats were going to cut the EPF's funding. Bishop engineered a false invasion to prove his organization's worth and receive funding. However, the false aliens' genetic residue came in contact with local wildlife, mutating them into a more savage, near-sentient form. The EPF and the Turtles used a lot of effort to contain the outbreak but had little success. With Leatherhead's help, the EPF were able to come up with an antidote, which they dispersed all over New York.
The EPF soon found Nano, believed to be a leftover alien technology, but was actually a government project. Stockman reactivated Nano's piece but the bots simply compiled all the technology in the base before going on a rampage.
When the original Shredder transformed New York into a city of nightmares, the EPF was busy trying to hold off his zombie minions. Unbeknownst to them, the Turtles had gotten rid of the zombies and had the EPF join forces with them, the Purple Dragons, the Justice Force, the Foot Clan and the Ninja Tribunal Acolytes to fight against the ancient menace.
In the mid 21st century, it becomes apparent that numerous alien species considered Earth habitable. The EPF rounded up aliens and extracted their DNA to create Organic Mousers, as named by Stockman, to counter against a potential invasion. But when Stockman tried unlocking the secrets behind alien life, he accidentally triggered a cataclysm that destroyed the lab. Bishop, who was pinned down by debris, was saved by one of the alien escapees. He soon realized that if one alien had mercy enough to save his captor, then others can do the same. So Bishop altered his views to Earth's defense. He eventually made the EPF into the Pan Galactic Alliance to liberate alien civilizations that have been fleeing alien civilizations due to tyranny. He made alliances with other races, uniting them into the Pan Galactic Alliance.
Thanks to years of collecting, and help from the Federation, the EPF is armed with multiple types of technologies.