Code Red joins Captain America Civil War is a future project to be made by RedSilver01 and Transformersprimefanfan.
In 1991, the brainwashed super soldier James Bucky Barnes is dispatched from a Hyrda base in Siberia to intercept an automobile carrying a case of super soldier serum.
IN the present day, approximately one year after the defeat of Ultron in the nation of Sokovia at the hands of the Avengers and Code Red, the teams - which now consist of Avengers Steve Rogers, Natasha Romanoff, Sam Wilson, and Wanda Maximoff and Code Red Members Nighlock, Red Smoke, Light Ultron, and Taser - learn that Russian mercenary Bane, plans to steal a bio weapon from the Institute of Infectious Diseases in Lagos, Nigeria. After being cornered, Bane commits suicide with a bomb in an attempt to take Rogers and Agent Tavary with him in an act of revenge. Maximoff and Taser contain the explosion, but they lose control of their powers and inadvertently destroy a nearby building, killing several relief aid workers from Wakanda.
Subsequently, after giving a speech at MIT, Tony Stark is confronted by a grieving mother whose son was killed in the Avengers' battle with Ultron in Sokovia.
One month after the incident in Lagos, Nigeria, in both their head quarters, the Avengers find Stark and Secretary Thaddeus Ross, in the New Avengers Facility, and Code Red finds Lykos and General Maximoff, both who retired from the team, waiting for them. Ross and Maximoff explain that due to the events in Lagos, the United Nations has decided that they can no longer operate privately. At first, Nighlock readily accepts this, but then he realizes that he will be forced to do something he already does. To that end, it has been decided that the Avengers and Code Red will sign the "Sokovia Accords", which will establish an international government body to control the Avengers and Code Red's movements as well as monitor and police the rapidly growing number of superhumans.
The teams are divided over the act; Stark, Lykos, and Maximoff support government oversight because they feel guilty for their roles in creating Ultron, whereas Rogers worries that the Avengers may be compromised if it comes under the control of a third party after the infiltration of S.H.I.E.L.D by HYDRA. Nighlock agrees with Cap, saying that Xode Red shouldn't even have to sign papers that tell them to do something that they already do. Ross states that refusing to sign will be seen as a sign of resignation.
Meanwhile, retired HYDRA Agent Vasily Karpov is ambushed by Helmut Zemo, whom Dash-9, Diesel 10, Splatter and Dodge, Den and Dart, Evil Trixie, Emma Frost, and The Bowser Family work for, who asks for information regarding the 1991 mission. Karpov refuses, forcing Zemo to kill him.
During their debate about the Accords, Rogers learns that Peggy Carter has passed away in her sleep and leaves for her funeral in London with Sam, Nighlock, Major Malfunction, and Light Ultron. While there, they learn Sharon Carter was Peggy's niece as she delivers a eulogy about how one should never back down from what they believe in. This solidifies Rogers', Nighlock's, and Malfunction's decaion not to sign. Wanda finds herself confined to the New Avengers Facility, and Taser finds herself confined to Major Mansion, by Vision, Justice, and Deadpool, obstinaibly for their safety since feelings are running high after what happened in Lagos.
In Vienna, where the signing of the Accords is to take place, a terrorist bomb kills King T'Chaka of Wakanda. When security cameras reveal the culprit as Bucky Barnes, T'Chaka's son, T'Challa, vows revenge. Against Romanoff's advice, Rogers, Nighlock, Major Malfunction, Falcon, and Light Ultron decide to go behind Ross' back and bring in Barnes themselves. The New Allies hear of the situation, with Apocalypse noting that this could leave Earth defenseless if they don't try an stop anyone outside of this, including Equestria, Earth will fall. Following a tip-off from a grueling chase, Barnes is captured, and Rogers, Nighlock, Malfunction, Sam, Light Ultron, and T'Challa are arrested for obstruction of justice.
While Barnes is in custody in Belin, Rogers, Nighlock, and Malfunction argue with Stark, Lykos, and Maximoff about signing the Accords. A box sent by Helmut Zemo contains an e-bomb which turns off the entire city of Berlin's electricity, including the cameras and computers that were monitoring on Barnes. Barnes is released by Helmut Zemo, who uses HYDRA's trigger words to send him on a rampage. Rogers, Nighlock, Malfunction, Sam, Light Ultron, and Quicksilver, who had gone back to stealing things after his retirement, manage to stop him and flee. After coming to his senses, Barnes tells them that Zemo is headed for the abandoned HYDRA Siberian facility where he and five other Winter Soldiers were created using the formula he stole in 1991. Believing Zemo plans to release the other Winter Soldiers and unleash them on the world, Rogers calls upon Clint Barton for aid in freeing Wanda, which Barton agrees to since he feels he owes her a debt since her childhood friend, Graydon Creed, saved his life in Sokovia. He manages to break into the New Avengers Facility and releases Maximoff, who uses her powers to overpower Vision. Nighlock and Malfunction call upon Indominus and Angelica Jones for aid in freeing Taser, which the two best friends agree to since Taser doesn't deserve such a punishment. Indominus and Jones break into Major Mansion and release Taser, who uses both her telekinetic and electric powers to overpower Justice and Deadpool. Falcon decides to recruit Scott Lang to join the Avengers, having been impressed with his abilities in their brief fight. Light Ultron decides to recruit Blue Eagle from the Airforce, knowing he would never stand for what the government is doing. Both are in awe at getting to meet Captain America, and quickly agree to Rogers, Nighlock, and Malfunction.
Stark convinces Ross to let him bring in his renegade comrades. Lykos and Maximoff agree. Tony recruits Romanoff, T-Challa, James Rhodes, and Vision. Some of the engines join as well. Percy and some of the other engines join Cap. Karl and Susanna recruit Red Smoke, Charlie White, Air Strike, Justice, and Deadpool. Feeling he is still undermanned, Stark visits New York and meets Peter Parker, a crime fighting vigilante with spider powers. When Stark asks him why he's doing this, Parker says he knows the price of not doing the right thing. Feeling they are still undermanned, Lykos and Maximoff visit Bayville, where they find James Sunstar, who has gone back to his original job as an illusionist and occasionally does a few assassination missions. When Lykos asks why he does this, James tells them he feels he's putting his talents to waste if he doesn't do his usual job these day.
With the team's assembled, Stark, Lykos, and Maximoff confront Rogers, Nighlock, Malfunction, the Team Cap, and Team Nighlock/Malfunction at Liepzig Airport alongside his new allies. In the distance, Mistress 9, Diesel 10, and Evil Trixie manipulate the fight. Apocalypse, Selene, and Jean Grey go to take out the three villains. When Togers, Nighlock, Malfunction, and Percy refuse to back down, the Avengers, Code Red, and engines get into a huge fight. The youngest of the New Allies keep the ponies off of them, with both Ratchet and Fluttershy seriously hurt. During the fight, Team Cap and Team Nighlock/Malfunction decide to buy Cap, Nighlock, Malfunction, Barnes, and Pietro time to get to the jet, at the expense of being arrested. Ant-Man uses his suit to grow into a giant. The escapees are confronted by Romanoff and Red Smoke, but they can't bring themselves to bring them down and let them escape. The rest of Team Cap and Team Nighlock/Malfunction are captured, and some of the New Allies are captured by the Element Bearers, including Breakaway. As Stark, Lykos, Maximoff, Rhodes, and Air Strike chase the jet, Vision attempts to blast Falcon and Justice and Deadpool attempt to blast Light Ultron, who are following them, but they miss and hit Rhodes and Air Strike and they plummet to the ground, with one paralyzed and the other having already transferred his mind into a computer should something like this happen. Romanoff and Red Smoke, knowing they will be arrested for acting against the Accords, go into hiding. Parker and Sunstar injured in the fight, and a grateful Stark sends Peter home, while Lykos and Maximoff bring James back to the Mansion, much to Parker's dismay. Apocalypse then kills off Mistress 9 to prevent the Equestrains from capturing the jet.
Stark, Lykos, and Maxiom off find evidence that Barnes was framed by Zemo, and finds that the rest of the Avengers and Code Red have been thrown in prison. Heading there, they disable a security camera and learn from Wilson and Light Ultron where Rogers, Nighlock, Malfunction, Barnes, and Maximoff are going.