Some time after the Doppler Town incident, Dr. Cain decided that another group of reploids (dubbed Repliforce) should be formed to help assist the Maverick Hunters and help lighten the load of dealing with Mavericks.
Though they were not originally designed to operate with the Maverick Hunters they did work together on a few cases. Cases which ultimately lead to Iris and Zero meeting. For a time things went very smoothly with both the Maverick Hunters and Repliforce working to protect the world.
Though soon enough a massive incident sparked a crisis for Repliforce. A massive floating city named Sky Lagoon was soon attacked by mavericks. Mavericks had managed to sabotage the power systems for the city and caused it to crash into the city below… killing thousands in the process. Unfortunately for Repliforce they (Colonel) were present in the area. Pressure was put on them to answer some questions regarding the incident. But instead of co-operating and disarming to answer the questions they instead chose to keep their weapons and maintain their innocence.
The leader of Repliforce, a massive reploid named General soon declared that they were innocent but the suspicion was unwarranted and insulting. And that they wished to break off from their Human masters/government and form their own independant nation. However, government officials took this as a sign of rebellion and quickly called in the Maverick Hunters to deal with the situation.
Both X and Zero were dispatched to deal with Repliforce's key forces. X being assisted by Double and Zero was assisted by Iris. They each attempted to deal with a few of Repliforce's squal leaders. But they refused to co-operate and instead attempted to fight. After a few were defeated, Colonel showed up. Zero confronted Colonel to try and persuade him to stand down and answer questions. But he wouldn't budge which prompted Zero to engage in a fight to force him to stand down. Though Iris showed up before the fight could really escalate and begged both Zero and Colonel to stop fighting and live in peace. Both Zero and Colonel decided to heed Iris's words this time and left in peace.
Though shortly thereafter when X tried to talk to Colonel, he refused to listen to X and X was forced to fight against him. X managed to fight Colonel to a standstill before he retreated to make preparations for their departure.
X and Zero continued to deal with their forces to try to get them to surrender and resolve the situation peacefully. But each one refused. To make matters worse, the hunter who had originally reported to X that Sky Lagoon's power core was damaged (Magma Dragoon) turned out to be the maverick responsible for sabotaging it and destroying the city. All so he could have the opportunity to fight X and Zero. He was deftly defeated, though his death did not ease the minds of X or Zero.
Finally X and Zero managed to deal with all Repliforce's squad leaders and rushed to the launch site. They encountered Colonel again and Zero engaged him in a fight. This time Iris was unable to stop them from fighting to the bitter end and Zero ended up killing Colonel. X had taken the time to try to get onto one of Repliforce's ships which were headed into space. But he was unable to get on board.
Taking a ship themselves X and Zero rush off after Repliforce. They manage to dock at the main ship, a massive space station/satellite with a powerful laser cannon. X and Zero break off to search for General to try and stop him. Along the way X runs into Double, who reveals that he's a maverick spy who's been plotting against X. X manages to kill Double. Zero, meanwhile, runs into Iris. Iris is distraught over her brother's murder and has collected his weapon core. She interfaces with it and transforms into a massive robot ride-like form and does battle with Zero. Zero managed to defeat Iris's battle form… however it came at a terrible cost. In the fight he struck her power core and dealt it a critical blow. After exchanging a few words with him, she died in his arms.
X and Zero proceeded onward after their respective battles. They met up and fought General together. Together they managed to easily defeat him, but before they could deliver a finishing blow the space station's main laser started to power up and was targeting Earth.
It was then that Sigma revealed himself as the mastermind behind everything. (Ordering Magma Dragoon to attack Sky Lagoon to cast suspicion on Repliforce. While he had approached Repliforce and warned them that the Humans and Maverick Hunters were planning on turning on them and that they should be ready to leave just in case. Thus causing them to doubt the humans.)
X engaged Sigma in battle once again while Zero broke off to stop the laser from firing. X managed to stop Sigma but Zero was unable to reach the control room in time to prevent the weapon from firing. Fortunately General, who although heavily injured, had gone out into space and collided into the laser cannon just before it's beam could get very far. This caused a chain reaction which started the space station to self destruct. X and zero hightailed it off the ship quickly before the entire thing exploded into nothing.
From this point, with most of Repliforce's command structure killed, Repliforce was left leaderless and directionless. So the entire group was basically dissolved. Remnants of Repliforce split off to follow their own paths. Some joined the Maverick Hunters while others joined other military groups, some became bounty hunters, others retired and some simply vanished.