"Pilot" is the premiere episode of Project Cadmus
In the town of Lakewood, Wyoming, a man named Mitchell Black goes into a liquor store to buy some booze, when suddenly, he hears the roar of police sirens surrounding a building. He runs outside and sees a group of terrorists on the roof of a skyscraper, with a bomb attached to a post with hostages tied to it. The terrorists then get ready to take off in a helicopter. Mitchell makes sure no one sees him as he runs into an alley and pushes a button on his backpack, causing it to transform into a suit of armor around him. He then flies off toward the roof of the building where the terrorists open fire on him, but the bullets bounce off his armor. He then takes out a few of the terrorists, but the rest escape in the helicopter. He then heads over to the bomb and communicates with someone through his helmet about how to disarm it. He manages to disarm it under a minute and then flies after the helicopter and takes out the controls, causing it to crash onto the skyscraper roof. But he manages to grab the last few remaining terrorists before the helicopter crashes. He then unties the hostages and ties up the terrorists. When a civilian asks him who is he, he tells him he goes by "Peacemaker". He then flies off, but, unknown to him, a man in the crowd below records him on a camera and reports back to his base.
At an unknown Cadmus building, Dr. Eobard Thawne finds himself in a dark room, being interviewed by Amanda Waller. Eobard turns out to be a physics and chemistry expert and is being interviewed to work for a special Cadmus team. When Eobard passes the interview, Amanda shows him to their HQ, which amazes Eobard. Amanda then introduces him to the rest of the team, Professor Anthony Ivo, a robotics and engineering expert, the chief of security and field operative, Jim Harper, Dr. Mark Desmond, a genetics expert, and Dr. Amanda Spence, a biochemical expert. Amanda then welcomes him to Cadmus and tells him that Cadmus was created after the rocket ship crash in Smallville, Kansas 23 years ago to defend against aliens and superhumans and metahumans and weaponize them. Jim then informs Amanda about the recent capture of the terrorists by Peacemaker. She looks up Peacemaker to learn more about him, but she finds no info available about him, no name, no social security, credit cards, address, birth certificate, etc. She then orders Jim, Ivo and his agents to investigate the scene. Eobard volunteers to join to gain some experience, which Amanda approves. At the scene, Jim has his men secure the perimeter while Ivo manages to retrieve a couple components of Peacemaker's suit while Eobard looks around in awe and manages to find chemical traces of the armor and copies them down to study later and reports this to Jim and Ivo. Back at base, Ivo analyzes the robotic components and finds it to be made of a Kryptonian metal from Brainiac's ship. He tries to trace the source of the metal, but is unable to due to a high-security encryption blocking the location.
Spence then studies the chemical traces and finds traces of kryptonite in the metal. Amanda then calls an emergency briefing to discuss their situation. Meanwhile, at a secure building, Mitchell is receiving his daily analysis and physical and is told by a scientist that he seems to be getting stronger. But when Mitchell walks away, the scientist tells Dr. Hank Henshaw, the man behind Project Peacemaker, that the kryptonite in Mitchell's system and powering the suit is chemically altering his body chemistry and that he doesn't have much time left to live. Hank though tells him to make Mitchell comfortable until he can find a solution. Mitchell though sees them talking, but he can't hear anything, but he suspects that they're hiding something from him. Back at the Cadmus base, Amanda calls Desmond away from his work, which he's very mysterious about and claims to be for the Cadmus genetics department. Amanda tells them that this Peacemaker seems to be part of secret government agency, similar to Cadmus, and must be stopped before they come a threat to the planet. She then suggests they set a trap for Peacemaker so they can find answers. She then assigns their positions, she assigns Eobard as the bait, Jim as the muscle, and the rest of them to build a containment unit for Peacemaker, which Spence, Desmond, and Ivo immediately get to work on. Eobard tries to get Amanda to not make him the bait, but Jim assures him that he'll be fine. Later, at an abandoned warehouse, Eobard is tied up beside a bomb and starts screaming for help. Peacemaker arrives to save him when suddenly, Jim appears in his own suit of armor, which Eobard refers to as his "Guardian". Eobard then escapes from the trap while Jim takes on Peacemaker. The 2 seem to be evenly matched until Peacemaker breaks down in pain, allowing Jim to take him out and has Ivo and Desmond load him in a level 2 containment prison. Back at the base, Amanda interrogates Mitchell and when he refuses to cooperate, he has Jim viciously beat him. Eobard watches this in horror and tries to stop it but Ivo stops him and tells him that this is how Cadmus works and it's for the greater good, which Eobard reluctantly accepts. Spence then goes over to talk to Desmond, but finds him working on something.
Desmond claims it to be nothing, but when Spence presses him for answers, Desmond yells at her to stay out of his business. He then loads his work onto a flashdrive and leaves. Back in the interrogation room, Mitchell ends up mentioning the organization he works for as Checkmate and tells them that he volunteered to be their test subject to pay off his gambling debt to Intergang and then starts becoming aggressive and attacks Jim. Amanda though sedates him and has Spence study his blood sample. Spence studies it and tells her that due to the kryponite injections, it's increasing his adrenaline and nerve reactors making him aggressive, but it's also killing him and that he's got about 12 hours left to live. When Mitchell hears this, he becomes furious at the scientists for using him as a guinea pig and killing him and escapes from his restraints. Jim tries to stop him, but Mitchell, due to the kryptonite in his system, has enhanced strength and manages to defeat Jim and then escapes in the Peacemaker armor and takes Eobard hostage. Amanda though reveals that in the sedative was a tracking device and then has Spence immediately get to work on a cure for Mitchell. When she finished, she gives it to Jim to use on Mitchell and has him and Ivo try to track him down. Meanwhile, Amanda tries to research Checkmate, but is unable to find anything. Spence then talks to Desmond about what happened earlier and apologizes, but Desmond apologizes to her and the 2 hug and make up, but Spence manages to steal Desmond's flashdrive. Jim and Ivo follow Peacemaker and Eobard and try to get them to land. Amanda though orders them to fire at him, but Jim's worried that he might hit and injure Eobard, but Amanda orders him to fire anyway and they fire and manage to damage the armor, causing them to crash land. Jim then aims the cure at him, but Mitchell holds a gun at Eobard's head. Ivo though manages to convince him to lower his gun, allowing Jim to fire at him, which cures him and knocks him out. They then take Mitchell and head back to base.
Once at base, Eobard angrily confronts Amanda for being willing to sacrifice his life, but Amanda tells him that it was a necessary sacrifice and that if he wants to be a part of Cadmus, he'll need to learn to make sacrifices. Spence installs Desmond's flashdrive into her computer and tries to find out what Desmond's working on, but finds it encrypted, causing her to vow to break the encryption. Amanda then has Mitchell sent to Cadmus HQ for further testing. That night, Jim has nightmares about his death, which he doesn't remember, causing him to bolt awake, wondering what these visions mean. At Checkmate HQ, Hank reports to his superior, "the Black King" that they managed to salvage the Peacemaker armor, but their test subject has been captured by Cadmus. The Black King though reassures him that they can find another suitable test subject for the Peacemaker armor and that Cadmus will soon no longer be a problem.