The game begins where Disk 2 ended. One year later (2948), The allies find themselves in a huge fight against the Ultranationalists and the Al-Kadhum for Universal takeover.
David Capone is brought to the Indiana State Prison. Vincent Mancini and an Unnamed Mafia Hitman overpower several guards and free members of their gang including David Capone. The jailbreak goes off with extreme violence. A shootout ensues as the gang makes its getaway they drive to a safehouse and ambush the cops.
The evil team then goes and have a conference at the Sears Tower in Chicago, they are then ambushed by the U.S. Army Rangers and the allies. Making their way to Chicago, the allied forces pursue them through the streets but are unsuccessful in stopping them. The war has broke out again. Dimitri Khrushchev is the new leader of the Ultranationalist Party and is willing to do anything to get what he wants along with Muhammad Saf-Halad, the new leader of the Alkadhum. Russia retaliates with another massive surprise invasion on Sangheilios much more powerful than the first after bypassing its early warning system, revealing that the ACS module had already been compromised before its retrieval.
During the invasion of Sangheilios, The Al Kadhum invade Zuka's home. He is unaware of what is going on at the time, but by the time he relizes, it's too late! They take Zuka's family and kill them, right in front of him. He is taken to the Sangheilian International Airport, and while driving there, he views his homeworld, burning, and collapsing before him. He arrives only to be escorted onto a helicopter, where he sits next to his arch enemy, Muhammad Saf-Halad. He then must endure the hardship of the smokey air, and Muhammad's story.
David Capone then hires a Hitman (Unnamed Mafia Co-Worker) to carry out his deeds of taking out other rival gang. He believes that their is a Mafia gang in Jackson Blvd robbing his corporation of money, he has no choice but to send him out on a suicide mission to take back the corporation and use the money to pay off the depts of the Ultranationalists favor for getting Xel Vaxum. The himan arrives at the corporation and gets caught in a crossfire, ending the fight fast he makes his way to the Board of Directors and meets face-to-face with the leader of the Unknown Mafia group. The hitman then shoots him in the head saving the company and the bosses life. The boss then repays by offering him to take as much as he wants, he takes all of it, a total of $50,000. He then exits the building and gets into the car, but as soon as he starts the ignition it blows up (Car Bomb). Emergency services then arrive and David Capone watches this from the news. Angered by what he believes to be a Mafia gang attack he decides to rob the United States Treasury in order to pay up the Ultranationalists.
The Broadway Mafia arrive at the Treasury, they get in quick and steal as much money as they possibly can, they take a total of $500,000,000. They manage to escape through the front entrance due to heavy resistance through the back. They head back to the safehouse in Washington D.C. and decide to hang out and stash the cash in a vault, and later move it to the white house when David Capone plans to take it over.
Back at Sangheilios, The Sangheii Marines, Keros Demons, Michael Konar, and Andromeda Vadum are then held captive at an Extermination camp for two hours. During their imprisonment, Khrushchev plans to use Pvt. Zuka Chavamee as a tool to take out the rest of the allied forces. Shortly afterward, Pvt. Zuka refuses his offer and is sent back to his cell where "he can rot". The team then sparks a prisoner uprising to escape the Extermination camp.
In Washington D.C. Pvt. James Connar and Sgt. Brian Bacon have been and summoned to the White house along with the allies. After touching down, they meet Mathew Wilson in a limousine convoy, which brings them to Whitehouse offices.
Pvt. James, Sgt. Brian and Mathew Wilson walk through the White house offices, clearing four checkpoints. Pvt. James tells in the present that he felt like he was being watched, receiving the chilling response that the Broadway Mafia were in the White house disguised as Secret Service agents, watching him.
After passing through the hallway, the allied forces meet President David Monroe. Monroe informs everyone that they must eliminate the evil team to protect the Universe.
Once the conference is over, all exit the whitehouse except for Xel Vaxum who is capture by the Broadway Mafia team wearing their Mafia uniforms and Balaclava masks for to keep their identity a secret. They grab Xel Vaxum and put a cloth over his mouth, giving him a sleeping agent and a Methoxyflurane injection. He then sleeps and they drag him to the car with an evil FBI agent who is undercover and plans to take Xel Vaxum to the toll booth for a quick assassination. On the way, he is ambushed at a toll booth and shot to death in his car but Xel Vaxum makes it alive. Xel Vaxum is then shoved out of the car and thrown on the floor where he sees David Capone and Vincent Mancini, who take Xel Vaxum to the Underground Facility.
Seize Control of the Ship.
Zuka awakes to find that he is in an Emergency Room. Unaware again, of what is going to happen. In this groosum, horrifying, terroristic, bloody/gory level, he must endure the pain, as well as the comments of The Doctor, and his co-workers. In the end, Zuka has had enough, and finally escapes, but doesn't seem to get real far, as Muhammad arrives and shocks him, a certain number of times, before he is finally tooken away to a cell. He awaits to be transported. Cold and alone, he has nothing to care for, except the thoughts that run through his mind about his family.
The Ballistic Marine Shock Trooper Squad continues to Arcadia, finding the ship completely functional, but abandoned. Exploring its inner depths, they realize that it is a trap set by Biochem to lure survivors, mainly Sangheili to the ship to conduct experiments on them. During the mission, Kairor receives a transmission from Khrushchev requesting to meet him at the capital in Washington D.C. to learn how to halt a nuclear threat that would release ChemX gas in the Universe.
Meanwhile, at the U.S. Army base Commander Steve Ramirez get a call to go to a local restaurant to talk about 'business'. At the dinner he meets with Vincent Mancini. During the dinner Vincent talks about what he is doing and reveals too much to Commander Steve Ramirez. Knowing that he wont get away he decides to take him hostage and sits him down until Backup arrives. David Capone and two other Mafia men come in the diner and David Capone then throws Commander Steve Ramirez to the ground and a Mafia member knocks him out with the High Powered Tommy Gun. David Capone then picks up Commander Steve Ramirez and takes him to the car and locks him in the trunk and speeds off. Soon Pvt. James arrives in his car who is ambushed by the Broadway Mafia. He manages to kill them and get inside the restaurant who finds the Bartneder dead. Suddently Vincent Mancini begins to stranggle him with a Garrote Wire, but Pvt. James flips him and interrogates him. Vincent soon gives in to his demands and tells him where Commander Ramirez is located. He then gets ambushed by the Broadway Mafia, but manages to escape. He heads over to the airport and gets chased along the way, but he manages to destroy their vehicles with a plan. He then gets picked up by Helicopter and heads back to base.
In Washington D.C. David Capone infiltrates the White House. Capturing President David Monroe and killing him. David Capone assumes the identity of the President of the United States and takes control over the White House.
As the Sangheili Marines regain control of Sangheilios, by retaking the capitals, they manage to push through the Ultranationalist and Al-Kadhum forces and guide Hotel and Kilo teams to retake their homeworld.
Each allied team is on there own; aware that they has become a liability and could endanger those around them, they are struggling to survive and bring down the Biochem Corporation led by the sinister Fernando Hernandez and head researcher Dr. John Stenson. Meanwhile, traveling around the world through different apocalyptic ruins, they must fight to survive extinction against hordes of zombies, killer devourers and the most terrifying creatures created as a result of the deadly ChemX that has killed millions. Making their way to Washington D.C. they decide to split up and take back three of the most important place that the evil team could be hiding in; The Capital Building, The White House, and The Supreme Court. They all then decide to retake Washington D.C. and make their way to the White House, where they meet up with David Capone, who manages to make a quick get away. They then find out that all elevators have been cut off and must make their way to the capital building and head to the elevator which leads them to the Underground Empire. The teams then splits up to take on their enemies and save the Universe before time runs out.
The U.S. Army Rangers then move in and save Commander Ramirez and millions of civilians tied to ChemX bombs.
Save Zuka or Sangheilios
Fernando Hernandez then makes his way to the detention center once again and gets Andromeda Vadum and take him to the arena to test his skills and see if Khrushchev picked the right one. Andromeda battles a group of Shadow Ninja's and succeeds, but Pvt. Zuka arrives and finds a Hologram of Fernando. Pvt. Zuka attempts to punch him but he dodges it and shoves Pvt. Zuka back. Fernando then gives him a offer that if he can fight along side Andromeda and help out, he may let them go free, but as soon as they both succeed in the offer, Fernando smiles and shocks Andromeda Vadum killing him. Pvt. Zuka then gets angry and leaps to stop Fernando and slices his energy sword through the window. He realizes that it is bullet proof and the energy sword stabs a little bit though, making a slice on Fernando's hand. Fernando then kicks the glass, sending Pvt. Zuka flying back and falling back to the arena pit. Fernando's hand heals and he heads to his base. Pvt. Zuka then attempts to disarm the shock collar and gets unconcious. Andromeda Vadum then wakes up and revives Pvt. Zuka Chavamee. Once he awakes they leave the arena and make their way to the outside.
In the Mafia base, Kairor and the team must fight off the Broadway Mafia and find David Capone. Once found Kairor charges at him knocking him to the floor. The team moves in to take the kill but David Capone activates a trap which electicutes them, leaving only Kairor and David Capone. They fight on a big platform and move slowly down. David Capone then punches Kairor and shoves him out of the way knocking him over the endge. While he attempts to get back up David Capone gets a sludge hammer and causes major damage to Kairor, almost threatening his life. Kairor then retakes the Sludge hammer and knocks it out of Davids hands and it falls to the bottom. Still going on with the fight Kair soon disarms him and shoves him towards the ledge. David Cpone then looses his balance and grabs hold of the edge. Seeing that he thinks that the broadway mafia will not continue on in the future, he makes a dying declaration that he doesnt derseve to be in this world and commits suicide just before Kairor can save him. Still heading to the bottom he takes out his grappeling gun and grapples back up to the team and they begin to head out.
In the Ultranationalist Base, Pvt. Zuka, Pvt. West, Major Josh Konaree and three other Sangheili Marines are overlooking the base and what the Ultranationalists are doing. After that they find that they must stop the launch in twenty minutes and kill Dimitri Khrushchev.
In the Underground Biochem facility Lucas and his Ballistic team most make their way to the weather machine and disable it. Entering the weather room Dr. John Stenson drops his newly found cure project destroying the cure for the infestation, he escapes and summons the "Monitor" to defend the weather room. After the ballistic team defeats the Monitor they make their way to Fernando's main chambers. Michael and Triston Lorenzo, Ryan Kortiv, Cpl. Jacobs, and Lucas Kordin battle the super-powered Fernando and seemingly kill him. Fernando does not die, but rather regenerates and escapes by helicopter, activating the purge bomb in an attempt to destroy the Underground empire and kill the remaining survivors and the allied forces.
As soon as the allied forces escape from the Underground Facility in the attempt that may destory their lives, they see approaching Dark Op Soldiers in Assault Helicopters and the allied forces prepare a final stand which continues in Keros: Chronicles Disk 4.
- Andromeda Vadum
- Sangheili Marine Corps
- Michael Konar
- Major Josh Konaree
- Field Master Lex Norsan
- US Army Rangers
- United States Advanced Air Force (USAAF)
- Xel Vaxum
- Vax Xalum
- Xeltive Thade
- Lucas Kordin
- ONI Spartans
- Cpl. Jacobs
- Tristan Lorenzo
- Michael Lorenzo
- Ryan Kortiv
- Fernando Hernandez
- Muhammad Saf-Halad (Leader of the Al Kadhum)
- Dimitri Khrushchev (Leader of the Ultranationalist Party)
- David Capone (Leader of the Broadway Mafia)
- Vincent Mancini (Second in Command of the Broadway Mafia)
- Broadway Mafia (Mafia Crime Group)
- Dark Ops
- Ultranationalist Party
- The Al Kadhum (Iraqian military in Disk 3)
- Devourers (Parasites)
- Military Preparations
- Uprising (Mafia rise to power)
- A New Empire (Al Kadhum rise to power)
- No Russian Loyalist (Ultranationalist rise to power)
- Strengthen an Alliance (Villains Conference)
- The Chase (Good team chases evil team)
- Planetary Takeover
- Deadly Siege
- No Mercy!
- Revenge (Al Kadhum capture Zuka Anthanee)
- Hitman for hire
- Washington D.C. Ransom
- Prisoner Escapes
- Welcome to Auschwitz
- To Break Loose
- National Military Establishment Conference (Good Conference)
- Unfinished Business (Mafia gets Xel Vaxum)
- Seize Control of the Ship! (Ultranationalists get Andromeda Vadum)
- The Doctor is in! (Zuka Anthanee is torchured by Iraqi doctors in The Insane Asylum)
- A Lethal Invitation (Mafia sends invitation about a restaurant and captures Commander Ramirez)
- White House Takeover (Mafia go into the white house and take over the oval office)
- Retaking Sangheilios
- A Fortunate Retreat
- An Apocalyptic World (Tokyo, Japan)
- An Apocalyptic World (Shanghai, China)
- An Apocalyptic World (Beijing, China)
- An Apocalyptic World (Moscow, Russia)
- An Apocalyptic World (Chernobyl, Ukraine)
- An Apocalyptic World (Berlin, Germany)
- An Apocalyptic World (Amsterdam, Netherlands)
- An Apocalyptic World (London, England)
- An Apocalyptic World (New York City, New York)
- An Apocalyptic World (Annapolis, Maryland)
- An Apocalyptic World (Washington D.C., United States of America)
- Taking the Capital
- An Apocalyptic World (San Diego, California)
- An Apocalyptic World (Los Angeles, California)
- An Apocalyptic World (San Francisco, California)
- An Apocalyptic World (Sacremento, California)
- An Apocalyptic World (Las Vegas, Nevada)
- The Underground Empire
- An Offer You Can't Refuse (Save Commander Ramirez and millians of civilians wired to oil drums, with 3 mega bombs timed to release the ChemX.)
- The Final Decision (Save Zuka, or save Sangheilios!)
- Crowd Control (Andromeda Vadum and Pvt. Zuka Chavamee must battle thousands of Devourers in an arena, Fernando Hernandez watches in amusement)
- The Stash House (The Mafia's Base)
- Saf-Halad Operations Base (Al Kadhum Base)
- The Nuclear Silo (The Ultranationalist Base)
- Biochem Reborn (The New Biochem Base)
- Biochem's End
- The game is much like Call of Duty: Modern Warfare 2, The Godfather I and II (Video Game), Bad Company 2, the Fallout series and Resident Evil combined.