After a year long stalemate with the United Nations Earth military, the Space Revolutionary Army carried out a massive colony drop onto the Earth, killing 99% of the human population and plunging the world into a nuclear winter. Now, 15 years since the wars end, the Earth has finally started on the long road to recovery in an era known as After War. Garrod Ran, a boy born at the end of the war survived the harsh world by becoming a technician and capturing mobile suits to sell on the black market. After completing the capture of a Jenice mobile suit, he is approached by Reich Anto for a job, to rescue a girl captured by a Vulture captain named Jamil Neate. Successfully rescuing Tiffa Adill from the Freeden, Garrod heads to the randevu spot to find Reich Anto waiting for him to take Tiffa back. Noticing how terrified the girl is of the man, Garrod instead drives off with her, following her directions as they try to evade Reich as he chases them with a trio of mobile suits. Finding an abandoned base belonging to the United Nations Earth military, Garrod finds a GX-9900 Gundam X and climbs into the cockpit with Tiffa. Activating the Gundam, Garrod engages in battle against the three mobile suits to protect Tiffa.

Defeating Reich Anto, Garrod comes face to face with the Gundam Leopard and the Gundam Airmaster from the Freeden, and barely escapes the two professional pilots. As Garrod Ran and Tiffa Adill rest, information brokers spread out and sell information on the battle they had just seen and the appearance of the Gundam X. The pilots of different Vulture groups all track down and locate the Gundam X as Garrod and Tiffa try to make camp in the forest, only to force a battle between the young pilot and an army of mobile suits. As the Gundam X starts to falter due to the vast amounts of mobile suits attacking it, Garrod swears not to let Tiffa die, his words causing Tiffa to use her Newtype powers. Registering the Gundam with a lunar base, the main weapon activates on the Gundam X and Garrod takes aim as the captain of the Freeden tries to make contact with Tiffa to warn her not to let the weapon be fired.

The Frieden has approached Garrod, he tries to fire upon it with the satellite cannon but realizes it takes too long to charge for him to be able to shoot. Jamil runs out on top of the ship and fires a magnetic grappling gun at the Gundam X. Garrod flies back but Jamil already has the gun attached and is pulled to the gundam. Jamil opens the cockpit and the gundam automatically stops flying back. Jamil takes the gundam back to the Frieden after telling Garrod he has no right to have the gundam or Tiffa.

In the hallway, Garrod stops Witz and Roybea, telling them they must not leave. Witz says he'll be in pain if he doesn't move. Garrod tries to stop them and is kneed in the stomach. From the floor he grabs Witz's ankle, begging, Witz then kicks him in the face. Garrod wipes away the blood and stares at the two in disgust. Witz is confused by the look, and Roybea explains why Garrod acted the way he did with a theory on kids. When questioned if he supports him, Roybea says no because adults can't do that. Garrod sneaks up on the doctor, planning on putting him to sleep with powder. The doctor turns and says not to disturb his reading, and lets Garrod have some time alone with Tiffa. Garrod apologizes to Tiffa, saying it is all his fault. The doctor knocks on the door and says visiting time is over because someone is coming. Garrod leaves and bows his thanks to the doctor.

The Freeden dodges to the side, only taking a little damage on the side of the main engine. The other Vultures send out mobile suits to provide cover for the Freeden. Shagia sends Olba off and easily destroys several vulture mobile suits. Garrod tries to take the GX, but Jamil stops him. He asks Garrod why he is going to help, and Garrod says it is natural because he wants to help Tiffa. Jamil gives him the control unit and lets him go out to battle the ""mysterious gundam."" Jamil tells Kid that Garrod is better than him, because of his cockpit phobia. Garrod rushes out to save Tiffa, and the Gundam Virsago stops him. Garrod fights a defensive battle against the skillful pilot of the Virsago, and the Freeden crew wonders why Jamil is fighting so oddly until he walks into the room and confirms Garrod as the pilot. Garrod continues to fight, slowly getting more skillful as the battle progresses. Outside of a party that he is the very host of, Roybea seems to regret leaving the Freeden

A group of vultures takes parts from an old abandoned reactor and run away as the temperature rises, escaping to a safe distance before it explodes. The leader is Ennil El. Zacotte Dackonot approaches Ennil, congratulating her on her job for the day. He then shows her pictures of the Gundam X and Garrod. Her interest is sparked in him when she learns that he used to hunt mobile suits all by himself, she says she'll join the job and secretively gazes at the picture of Garrod.

Jamil reminds Garrod of the satellite cannon. They stop and Garrod gets the microwave and fires the cannon, propelling the two away from the blast. As Jamil's Daughtress grips the GundamX, a rock slams into its cockpit. On the Freeden, Shingo wonders if they survived. Sarah comes in asking about the Captain, and sees the Gundam X carrying the captain's Daughtress back to the Freeden. Jamil needs surgery and the Doctor says not to move the ship. Garrod tries to apologize, but Sarah slaps him. They then leave him. Garrod goes to visit Tiffa, but she doesn't want to talk or have him see her with lipstick on.

Zacotte's group of vultures continue to fry Witz. As he is about to lose consciousness, an aircraft flies down and attacks the mobile suits. The Airmaster transforms into fighter mode and leaves, waving a wing to the aircraft as a thank you. Inside, the Frost Brothers mock the thanks, saying that they weren't trying to save him. Garrod has Ennil at gunpoint, demanding that she admit she was going to kill him and steal the gundam. She tries to talk to him about being lonely, and he shoots over her shoulder in fear. He threatens to shoot accurate next time, and tells her to be gone. Upset, Ennil leaves the room and city.

Roybea wonders aloud to Witz if the two should commit a double suicide with the Frieden, but Witz says the treasure on the ship is too valuable. Roybea says he can't leave because he was hired. Suddenly a shower of beams hit the ground near the two. Roybea has a bad feeling about the attack, and his suspicions were confirmed by the Ashtaron's grabbing of his Gatling gun. The Virsago shows up from the smoke and Olba says (from the Ashtaron) that he can finally get his revenge. Witz and Roybea begin to battle the two, to prove that they are wrong in the assumption that they can gain their revenge.

In Fort Severn, Mayor Nomoa Long speaks and introduces the leader of the Army, Newtype Carris Nautilus. Carris said everyone must become newtypes with high judgment and recognition abilities, but the war killed out most of the race. He was born as one and plans to use his power for peace. On the way to Fort Severn, the Frieden's bridge discusses how fast they'll get to Fort Severn and the accuracy of Tiffa's drawing to it's picture. They then discuss what to do if Newtypes are found.

Carris pauses, beam saber held over the GX's cockpit. He tells Tifa that Garrod's life depends on her, and begins to lower the saber, heating the cockpit to a burning red. She exits to the roof and Carris takes her away. The Gundam X still lies helpless on the ground, and the other two gundams collapse as the bits leave them. Ennil grumbles about Garrod's survival, and then wonders why a Vertigo was there. In the infirmary, Witz and Roybea complain to Tonya and Sarah about their bandaging abilities. The captain comes to check Garrod, and he begins to scream in mental agony. They begin to talk about the newtype they came searching for beating them, and Witz begins yelling about saving Tiffa for Garrod's sake so he can calm down. While supervising gundam repairs, Kid has an idea and requests that Jamil let him upgrade the GX. Jamil agrees, and asks Kid to help Techs in a favor for him (curing his cockpit phobia).

The Divider's new thrusters on its shoulders fire, and the Gundam X falls face first into the snow. Everyone watches and wonders if Garrod will be able to fight well enough against the Frost brothers. The two enemy gundams attack, and Kid tells Garrod to use the Divider. He then pulls out the huge shield and uses it's thrusters to fly between the two charging gundams. The Gundam X then gains the upper hand in the battle, proving it's total upgrade. Jamil notes that Garrod is able to survive because he is a genius of adaptability and extremely talented at handling machines. Witz and Roybea join the battle, using head vulcans and other small damage weapons that they still have ammo for. The Frost brothers argue, Shagia saying that they've reached their limit and leave. Olba finally agrees, but changes his mind as they flee. He flies back and Garrod fires the ""harmonica cannon"" in the Divider shield, a blast aimed straight at the Ashtaron.

Just as Ennil is about to shoot Garrod, explosions shake the city. The fierce battle between the Gundam Ashtaron and the Gundams Leopard and Airmaster has shifted to borders of the fort's walls. Tiffa tackles Garrod and an explosion destroys the wall that was behind her. With Carris blown to the other side of the room, Garrod prepares to leap out of the window with Tiffa. Before doing so, he invites Carris to follow them. But the artificial newtype just stares at him in the confusion of wondering who he should trust by then. Garrod and Tiffa leap out of the 3 story window and fall into the snow. Ennil runs to the window to shoot the two as they run down the streets, but another explosion on the side of the building throws her to the floor.

Garrod shakes Carris lightly, telling him to hang on. He realizes there were no bullets in Carris' gun and asks why he did it. Carris is then taken prisoner, delivered immediately to the emergency room. In Fort Severn, a man tells Mayor Nomoa (Professor Dorat) that Carris was captured. The Mayor is infuriated by it. Carris survives on the Freeden, and Tiffa and Garrod are happy for his amazing survival. In Fort Severn, Professor Dorat has begun the energizing of the Patulia, and Ennil says she will retrieve Carris for him. Garrod wanders out of his room in the middle of the night, freezing cold. He notices blood on the floor and follows it outside. Tiffa shows up as he gets a jeep, and the two drive out in the snow to find Carris. They find him laying in the snow, and he tells them to let him die in the cold. Garrod then has to convince Carris that he wants him to live, even though the boy can't understand why Garrod would want someone like him. Suddenly, snowboarding mobile suits sh

The narrator speaks, "Fifteen years after the war which nearly destroyed the Earth, people started to rebuild their normal lives. But... in this world without order, there was still a hell where the strong prey on the weak." While he speaks a peaceful farming community is suddenly attacked by a group of vultures, which quickly kill all resistance. Witz and Roybea are waiting at a fork in the road, wondering what a sign says. Roybea suggests "Heaven and Hell." Witz says he hates people who say things like that, then insists that his side is Heaven. The two then part, going off on small vacations because of the taxation of being on the Freeden all the time when they were used to small intervals as free lancers. In the Leopard, Roybea has hundreds of red roses, which he says are for love. And a yellow one which is "special." He then decides to, "start with 'A's."

Tiffa has a dream about the beach, and she then wakes up to draw a rock formation she saw in her dream. Early in the morning, Shingo is doing business with a man who ordered 3 of their Daughtress type mobile suits, and the two make brief conversation on how people near the ocean are easily building up their cities. Around the same time, Garrod is carefully trying to make the perfect breakfast for Tiffa, getting fruits and such from the buffet in the Freeden's cafeteria. One of the reasons why I love the doctor comes now, Garrod begins to give his morning greetings to everyone. To Techs, he says, ""What's up!"" and gets the reply, ""The proper greeting is 'Good morning'."" He stops briefly and has a conversation when he notices Witz and Roybea are eating in, rather than away from the ship as they normally do. Garrod goes to Tiffa's room, to find her unconscious on the floor with a drawing nearby.

After watching the laser beam come from the sky, a white dolphin tells Tiffa that she hates humans. During the next day, Garrod tells Jamil of his sighting of the satellite system laser lock. It is concluded that this means there is another GX and newtype somewhere across ocean. Doza Bale orders the D-Navi(see terms) to be put onto every mobile suit in his ship, saying he wants to own Gundams to prove that he is the strongest man on the ocean. Around the same time, Garrod delivers Tiffa's food to her, suggesting that she try eating with the crew more often. He hears a horn in the distance, and sees a ship heading for them. Garrod then runs as fast as he can to his gundam, being stopped by the doctor who informs him that they are simply buying supplies from some sea vultures, and that what he sees is not an Orc ship. Kid speaks with one of the sea vultures, asking for an underwater scanner.

The narrator speaks, ""Near the end of the last war, a Federation unit was silently working on an important operation. Scientists researching Newtypes worked on this operation with utmost secrecy. It was named, ""Operation L."" If Operation L had been executed, the last war might have ended differently. However, the word ""If"" doesn't make sense if used to describe history. The existence of Operation L was erased form all records... along with the soul of a woman."" A ship floats idly in the ocean, men passing their time in recreation. Suddenly torpedos hit them from beneath as Marcus Guy's Orc group attacks them, making quick work and going straight for stealing the supplies. Suddenly Gundam Ashtaron surfaces and uses a claw to grab Marcus. He asks for the man to do a salvage operation for him in the sea of Lorelei. On the Freeden, everyone works to bring supplies on board from a sea vulture ship.

Free of the hold of the Ashtaron and of the mysterious power, Garrod lands a crippling blow to the Orc submarine, forcing it to surface and withdrawal along with Olba Frost. Going back to the Freeden, he learns that Tiffa has become possessed by the mind and power of a Newtype stronger then her, they mysterious woman on the Orc ship and the former instructor to Jamil Neate. She revels to all what happened to her 15 years ago shortly before the end of the war, and the crew agree to help Jamil free her from the ship and her capsule.

Damaged and short on supplies, the Freeden puts into port at Saints Island, and independent nation that is thriving because of a power station left undamaged by the war. After being inspected by the customs and immigration officier, Miles Goodman, the Freeden is allowed to stay at the island and the crew to get some rest. Sent out on her own to get most of the shopping done for the ship, Toniya runs across Ennil El, neither knowing who the other is.

Not impressed with the efforts of Colonel Aimzat to capture the Freeden, or his faith in Newtypes, the New United Nations Earth Committee members send as special operative to take care of the task of capturing the Freeden as well as Jamil Neate and Tiffa Adill. Katokk Alzamille, camouflages his team as fisher men whose boat was damaged by and in distress to gain access to the Freeden only to be escorted into a trap set by the crew thanks to the warning of Tiffa.

Stopped by Tiffa from turning himself into a human bomb, Katokk is placed in a room on the Freeden under armed guard and interrogated by Jamil Neate as to the location of the island base of the New united Nations Earth. But the questions change as they two start to talk about the war, and how the soldiers in the regular army called Jamil "Hero". While on patrol, Witz and Garrod find Ennil in the remains of her mobile armor, bringing both her and the black box to the Freeden for questioning and finding out the location of the base Zonda Epta.

Captured and imprisoned on the island, Garrod tells off Katokk, striking a nerve with the soldier and causing him to almost knock him out with one punch. As the crew of the Freeden is held in a cell, Jamil and Tiffa are taken to meet with Aimzat as he plans to move them to the Newtype Labs for research into their powers and abilities.

Guilty about her betrayal, and betrayed by Aimzat, Ennil helps the Freeden crew in their escape as Katokk helps Garrod get onto the transport ship carrying Jamil and Tiffa. As the battle with the escaped crewmen and women of the Freeden heats up on the island, Jamil and Tiffa make their own escape on the transport ship, rushing to get the control unit of the Gundam X to Garrod. Making their way into the cargo hold of the New UNE transport ship, Garrod and Katokk find the new Gundam Double X and are pinned down by enemy fire. Coming to their rescue, Jamil proves that his title as "Hero" is well founded as he takes out the soldiers at the door and allow for both he and Tiffa to get the control unit of the Gundam to Garrod.

After escaping from Zonda Epta and evading the New UNE Navy, the Freeden lands in a country in southern Asia called the People's Republic of Estard and are approached by its leader and generals to join with them in their fight against the New UNE military. At first declining the offer, the crew changes their mind after they survive and witness the aftermath of a large carpet bombing raid carried out by the New UNE on civilian areas.