Dr. Koopa's Repliforce

Dr. Koopa's Repliforce is a story arc in Freedom Fighters NEO. It introduces Iris, Slash Beast, Spiral Pegasus and many Repliforce members. 
== Plot ==
Sonic's friends were seemingly unaware of the fact Dr. Koopa died after piloting Gamma. However, shortly after that, an army of Reploids, which was calling themselves the Repliforce, stated it will destroy the Maverick Hunters, the friends of the Freedom Fighters, and that anyone in their way will be destroyed. Black Bat then comes in and says he already noticed the location of the members of the Repliforce, but they don't work for Robotnik. Sonic promises that he will spare them, but someone needed to knock some sense into the Repliforce. 
First, Sonic, with help from Cut Man, took out Web Spider. Cut Man tries to take him hostage, but Sonic convinces Cut Man to leave the Repliforce members to the Freedom Fighters. Then, Sonic faces Split Mushroom with help from Elec Man. Split Mushroom says that he wasn't working for Repliforce, but for someone meant to rule everyone and everything, who was NOT Robotnik, but an enemy of Dr. Koopa's father, King Koopa. Metallix then comes in and vaporizes Split Mushroom with his Spin Dasher, which was modified to be the weakness of any sentient non-Goomba fungi, and gives the news that Dr. Koopa is alive, which shocked Elec Man and confused Sonic, as he didn't knew that Dr. Koopa died.
Meanwhile, Nicole gets infected with a virus. Being Cyberniks, Tekno and Shortfuse manage to enter the cyberspace and stop Cyber Peacock, who was there to collect info about the Freedom Fighters for the Repliforce.
Tails, having became the best pilot of the Freedom Fighters, joins Sonic, using the Tornado to infiltrate Storm Owl's ship and interrupt a fight between Storm Owl and Zero. When Sonic asks their motives, Storm Owl says Zero singlehandedly wiped out the entire Repliforce. Zero says he didn't want to fight, but the Repliforce wouldn't listen to reason. Storm Owl then reveals that Repliforce was branded as Mavericks for no reason, and they couldn't just let their name tarnished. Sonic then realizes that both the Maverick Hunters and the Repliforce were wrong: the Maverick Hunters were wrong because Repliforce, who was fighting for their own rights, were Freedom Fighters, and the Repliforce was wrong because Freedom Fighters don't attack someone who doesn't want to fight. Dr. Koopa is then heard through the airship's speakers, stating that Repliforce wasn't wrong, that Zero actually turned the Maverick Hunters into Mavericks, and that the Hunters had to be destroyed for world peace to be achieved. Then he calls Sonic and Tails traitors for "siding with the real Mavericks" and sends Spiral Pegasus to destroy them. Spiral Pegasus firstly mentions a woman named Iris, and attempts to attack Zero, but he's stopped by a bat Reploid. Sonic identifies the bat Reploid as Black Bat, but then he reveals his real name is Dark Necrobat, and that he was working as a spy for a group of Anti-Mavericks. He took the facade of Black Bat to blend in the Freedom Fighters, and Magma Dragoon ordered him to destroy Dr. Koopa and anyone who wants the Maverick Hunters and the Repliforce to destroy each other: in other words, Spiral Pegasus, who was always jealous on Zero because of Iris' feelings for Zero. Sonic tries to stop Dark Necrobat, saying that Dr. Koopa is his friend, but Dark Necrobat replies with: "Someone who calls you a traitor can't be your friend" and leaves.
Sonic and Tails then try to confront Magma Dragoon, but when they reached the Anti-Mavericks headquarters, they only found Storm Eagle And Tornado Man, who were busy retiring Burn Dinorex. Storm Eagle explains that Dinorex was using some illegal weapons to force the volcano erupt and destroy "Dragoon's temple". Indeed, the Anti-Mavericks headquarters was more like a Japanese temple, but with plenty of devices for training in martial arts. Storm Eagle says he doesn't want Dr. Koopa or Repliforce to perish, as he can relate to them, and that he managet to make Tornado Man realize the truth. After Sonic reveals that Repliforce became a Freedom Fighter group after being branded as Mavericks, Eagle reveals that Dragoon was at Repliforce's arctic base, and he believes Dragoon was confronting Frost Walrus.
Indeed, Dragoon and Frost Walrus were calling each other traitors (as Frost Walrus started some riots unrelated to the Repliforce and mercilessly slaughtered some Reploids for no reason). Fire Man, who came to help Sonic and Tails, figures out that Walrus was wrong and sides with Dragoon. Upon Sonic and Tails explaining Repliforce's situation, Dragoon reveals that the Repliforce War was his fault, and that he believes Dr. Koopa brainwashed Repliforce into destroying the Maverick Hunters. He then says that the Rock Force was the only one who could free Repliforce from Dr. Koopa's control.
Two Repliforce commanders remained, and Sonic and Tails decided to split up and meet at Freedom HQ. Tails uses the Sea Fox to catch up with Jet Stingray while he was blowing up a Maverick Hunter base on the shore. Tails and Dive Man corner and capture Stingray.
While this was happening, Sonic and Nitro Man try to catch up with Slash Beast's train, but Nitro Man can't keep up. Luckily, Slash Beast had a vision of The Merger Magikoopa, who shows his dissapointment in Slash Beast. The Merger Magikoopa claimed that, by not questioning "the General's sanity", he doomed the Colonel's sister, who, as he claims, was the only one who could turn a certain Maverick over a new leaf. This vision makes Slash Beast realize that Zero could change, despite Dr. Koopa's belief, and then Beast tells Sonic that there's no reason for them to fight.
After Sonic and Tails returned to Freedom HQ, Web Spider and Jet Stingray were into custody, Frost Walrus was dead due to his crimes for which Magma Dragoon and Fire Man executed him, Spiral Pegasus was dead too because Sonic thought he was utterly insane, but Storm Owl and Slash Beast were still out there, questioning Dr. Koopa's sanity. Dr. Koopa then sends the Freedom Fighters a message, telling him that he has a top secret project ready to be transported to his sun system, and that if the Freedom Fighters really are his friends, they wouldn't interfere. Sonic and Rock, however, decide to confront Dr. Koopa, although Sonic manages to convince Rock to spare Dr. Koopa. Unfortunately, they're encountered by the Colonel of the Repliforce, who wanted revenge against Zero. Sonic takes the Colonel into custody, with Colonel complaining that he was so close to reuniting with his sister, but Sonic and Rock ruined it. 
Dr. Koopa then states he wanted to meet Zero at Bowser Jr's Robot Reactor, which was actually his sun system, and that Zero had to come alone. Metallix, however, took Sonic with him and went there, as he was questioning Dr. Koopa's sanity. Zero then reveals his top-secret project as "Project:Iris", a Ride Armor-like being with a purple color scheme and a pair of wings. Dr. Koopa then says that if he knows what's good for Project:Iris, to which he refers as "her", he'd die, and orders Project:Iris to kill Zero. Project:Iris easily overpowers Zero, who did nothing at all to fight back, but before she could land the killing blow, Dr. Koopa was knocked by Sonic right into Metallix's Spin Dasher. Despite this fact, he still keeps conciousness for long enough to question why was Project: Iris hesitating all of the sudden, to which she replies: "Ze...ro..." Afterwards, she turns against Dr. Koopa. However, in a last ditch move to give Zero a heart attack, he destroys the Ride Armor with "Soul Body", a technicque Metallix never expected Dr. Koopa to use. Luckily, the Ride Armor was merely a shell, revealing the real Project:Iris, who was both the Iris Spiral Pegasus mentioned and the Colonel’s sister. Iris lands in Zero’s arms, but a mysterious figure appears behind Zero. It turns out to be Layer, a female Reploid who had a crush for Zero and who was hunting down Dr. Koopa because he wanted to kill Zero. To do so, she upgraded herself with some parts from one of Sigma’s older bodies. She also wanted to make sure that Iris will be completely destroyes, so Zero could be hers and only hers. Metallix then starts wondering if Amy Rose would turn out like Layer. Layer manages to overpower Sonic, but she’s then attacked by Dr. Koopa, who was contacted by Slash Beast and Storm Owl, saying that, if Zero’s "inner Maverick" is destroyed, then Project:Iris would succeed, and that the Repliforce did a mistake by confronting Zero. Layer claims that Iris was on Repliforce's side and that she never truly loved Zero, but Dr. Koopa replies: "So, you're saying that she wanted a war which she knew it will have as consequence her demise, due to her being caught in the crossfire, happen? Regardless of how you'll answer this question, you're wrong." Dr. Koopa then kills Layer and apologizes to Zero, stating that he made a misjudgement and that he only went rogue because of Zero's actions during the Repliforce War, including what happened to Iris.
The next day, Dr. Koopa formally apologizes to the Maverick Hunters and states that, while both the Maverick Hunters and the Repliforce are strong, they are stronger together, and that they should use their shared power to free Mobius from any Maverick activity, calling Robotnik "the real Maverick." Zero and Iris weren't present: Zero was wondering if what Layer said is right, but Iris confirms that Dr. Koopa gave the answer that was the closest to the truth, and that she never wanted the Repliforce War to happen in the first place, that being her motive behind her constant pleas to stop fighting. Zero reveals he tried to reason with Repliforce, but they didn't listen to reason, and that's why he killed the Colonel. Iris thanks Zero for trying his best to not fight Repliforce, and apologizes if she hurt him after Colonel's demise. Zero states that the only thing that was hurt was his heart, but that was worse than Sigma blowing him in half. The two then share a kiss.