The new White Base battleship docks in the remote colony of Side 7 to conduct final tests from the prototype mobile suits. Zeon becomes aware of Operation V and send out a detachment of troops under Char Aznable to assess the extent and progress the Federation has made. The Federation become aware of the Zeon presence and issues orders for its citizens to evacuate into shelters. A few of Char's men infiltrate Side 7 in mobile suits and attempt to gather information on the Federation. Gene, one of the soldiers, disobeys orders and attempts to destroy them instead of wait for Char's orders. The attack leaves the whole colony in panic and the Federation tries to salvage as much of the prototype mobile suits and weapons and evacuate into the White Base. Amuro Ray tries to gain permission for the citizens to board the White Base, realizing that the shelters cannot hold out against the explosions, but along the way, he stumbles upon the Classified Operation V information and prototype Gundam. He then decides to activate the Gundam and fights the Zakus before they can attempt to destroy it, resulting with one of the Zakus to blow a hole in Side 7's wall. Char decides to then to approach Side 7 in Dren's battleship and open fire on Side 7. The whole incident comes at a heavy cost. Char loses Gene and Denim, but Gene manages to destroy many of the prototypes and inflict heavy personnel casualties on the soldiers and citizens in Side 7. As a result, the only survivors are the refugees that boarded the White Base, Amuro himself, and few Federation personnel, although most of them are new recruits. Amuro manages to salvage the remaining prototypes: a Guncannon and Guntank.
Before leaving Side 7, Sayla Mass and Frau Bow go for a last round to look for stragglers. Char, with a small group of soldiers, infiltrate Side 7 again to gather information from the wreckage caused by the previous attack. Sayla then stumbles upon him, and Char realizes that she resembles his long lost sister, Artesia. Their meeting is cut short as Char is also discovered by Amuro, who was on a mission to destroy what could not be salvaged. Char then retreats outside Side 7 and boards his personal Zaku and shows Amuro how an ace pilot fights. Realizing that their firepower is ineffective against the new Gundam, Char and his remaining men retreat. The younger refugees become volunteer crew members and pilots and the White Base departs for the Federation outpost Luna 2. However, they learn upon arrival that they are ordered to descend to Earth and go to Jaburo base and their stay is short. The soldiers of Luna 2 are unable to take care of the refugees and provide little resources and support, showing that the of Federation forces in space are cornered and are on the defensive. This meant that the White Base would continue on with the same crew of young, inexperienced soldiers and volunteers. Their only experienced member, Captain Paolo Cassius, is taken into Luna 2 for the wounds suffered during the attack and the new Captain, Bright Noa, is forced to take his place by default despite his low officer rank.
During atmospheric decent, they are attacked again by Char and his troops, and in the disarray of the battle, Amuro is distracted enough to be dragged into the atmosphere. Luckily, the Gundam is capable of atmospheric entry on its own, but in a panic, Amuro's decent path is changed towards Zeon territory in North America. Bright Noa has no choice but to follow Amuro since his orders required both the Gundam and the White Base to arrive in the Federation's secret base in Jaburo. Now trapped in Zeon territory and now under attack by Garma Zabi, the crew members receive "new orders" to escape towards the ocean and then head to Jaburo. The crew now realize they're in deep in enemy lines, and the Federation will probably won't send any help. In the midst of battle between the White Base and the combined forces of Char and Garma, Lt. Matilda arrives under the orders from General Revil. Unfortunately, she can only offer the crew a quick resupply and tells them to escape to the west. During this time, Amuro begins to become infatuated for Lt. Matilda. She then leaves the White Base and they are back to becoming decoys for the Federation on Earth. Tired of running from Zeon, Bright decides to use the darkness of night and a partially exposed sports dome to hide the White Base and its mobile suits for an ambush. Char sees through his plans, but doesn't tell Garma in a plot to get him killed. Bright executes his ambush successfully, and Garma, realizing that Char has left him to die, takes his Gaw battleship and attempts a final kamikaze attack. He dies in vain.
The White Base, now without Char and Garma pursuing them, decide stop and hide along a coastline. Amuro uses this time to fly a Core Fighter to his nearby home on Earth. He finds his home now occupied with drunken Federation soldiers and his mother missing. Luckily another person from the area recognizes him before he causes too much trouble for the soldiers there and takes him to the shelter where the rest of the townspeople are staying, including his mother. He discovers that the area is under Zeon control and the Federation soldiers have pretty much given up on contesting for control of the area. A Zeon patrol stops by the shelter to investigate the sighting of Amuro's Core Fighter and Amuro ends up exposing himself and the White Base to the Zeon in the territory. Matilda's ship is forced to come out of hiding to guide the White Base and do emergency repairs and resupplying. At the same time on Side 3, Garma's death reaches the rest of the Zabi family, and his death is used as propaganda to rally the citizens. The Zabi family also sends Ramba Ral and his troops on a mission to avenge Garma. Kycilia then begins to hunt and eventually locate Char, who has gone MIA since the death of Garma. The White Base crew have no choice but to keep running.
Still under the pursuit of Ramba Ral, Sayla this times sorties in the Gundam in an attempt to find out more about Char, the man who resembles her brother. The Gundam proves to be hard to control, and in the following battle, Sayla almost loses to Ramba's Gouf if not for the intervention of Ryu Hosei. Back on board the White Base, Sayla lies about the reason she went out in the Gundam, claiming she simply wanted to prove that a woman could pilot the Gundam and that Bright does not have to rely too much on Amuro. Bright sentences her to solitary confinement, where another Zeon captive, Cozun, from the previous battle provides her enough information to verify that Char is indeed Sayla's brother, Casval. Cozun takes advantage of the White Base's inexperienced crew to stage an escape and inform Ramba Ral of the mobile suits they are up against. Cozun also frees Sayla, thinking that she is willing to defect to Zeon. This leads to his undoing as Sayla informs Bright of his escape and he is killed during his escape of the White Base.
After the battle, Bright and Mirai Yashima discuss Amuro's attitude and were thinking about replacing Amuro with another pilot in hopes he would mature, but Amuro, performing maintenance nearby, overhears them and misinterprets their conversation. Disgusted with Bright and Mirai, he decides to leave in the Gundam without permission. Bright lands the White Base and Frau goes out to search for Amuro. Amuro hides his Gundam and goes into the nearby town for water when Ramba Ral's troops also pull in for a pit stop and a quick meal. Ramba Ral's lover Hamon takes a liking to Amuro and pitches in for his meal, and Amuro is shocked over the fact that he has been fighting against kind people. Frau is caught by Zeon troops guarding the entrance and exposes Amuro's identity as a Federation soldier. Ramba Ral lets them go, but also sends men to follow them to find the White Base. In the ensuring battle that follows, Amuro repels Ramba Ral's attack, but afterwards is placed in solitary confinement for leaving without orders. Ramba Ral receives new orders to capture the White Base as both the Federation and Zeon are mobilizing to battle in Odessa and the White Base serves as a vital wildcard for whoever controls it. Ramba Ral and his troops infiltrate the ship and engage the White Base crew in close quarters and hand to hand combat. The troops are unsuccessful in taking over the White Base, and Ramba Ral discovers Sayla, realizing that she is Artesia Daikun. He lets down his guard and Ryu surprises him from a corner and gravely wounds him, but Ramba Ral also manages to return fire on Ryu and wound him as well. With his operation a failure and nowhere left to run, Ramba Ral takes his own life.
Meanwhile, on the Odessa battlefront, the Federation is determined to take over Odessa and put a dent into Zeon's mining operation, putting them back on the offensive. M'quve decides to send his Black Tri-stars squadron to deal with the White Base. General Revil sends Matilda again to resupply and provide the White Base with the Core Booster, convinced that Amuro and Sayla are newtypes that are capable of turning the tide to the war. The Tri-stars rush to destroy the White Base while keeping Amuro distracted in the process. Amuro is unable to take on all three of the Tri-stars at once, and Matilda uses her ship to protect the White Base and dies. Amuro's newtype ability become more apparent as he is able to avoid their Jet Stream Attack and Sayla arrives in the Core Booster in time to help Amuro hold the Black Tri-stars and defeat them. The White Base gets little time to rest, as Hamon stages an all out suicide operation with the remainder of Ramba Ral's men on the White Base. Amuro desperately holds back Hamon's battleship, rigged to the brim with explosives. Hamon uses this opportunity to take down Amuro's Gundam, but a wounded Ryu sneaks off in a Core Booster and rams it into Hamon's Magella Top, killing them both and allowing Amuro to focus on protecting the White Base. Now with the Federation attacking from the front and the White Base from the rear, M'Quve abandons Odessa and launches into space with whatever resources he has left. The Federation now launch their own offensive after their decisive victory in Odessa.
The White Base now is docked in a Federation base in Belfast, where the crew are personally greeted by General Revil. Kai Shiden, a Side 7 refugee turned pilot, becomes tired of fighting and gains approval from Bright to leave the White Base under the pretext of shore watch. He then encounters Miharu, a Zeon informant that notifies Char of the White Base. Char, now back in Zeon forces after being reinstated by Kycilia, stages an attack using Kai's information he gave to Miharu. His guilt and concern for the other crew brings him back into battle and he helps them fight off the amphibious Zeon assault. Kai decides to board the White Base again, but not before finding Miharu in Bright's room, disguised in a Federation uniform. Miharu ends up leaking the White Base's position and destination, and upon seeing the orphans Katz, Kikku, and Letz, she begins to feel tremendously guilty over the fact she is putting other children in danger to feed her siblings. During the next Zeon amphibious attack, she asks Kai to board the Gunperry with him to fight off the attackers. The Gunperry weapon control circuits were damaged in the middle of the fight, and Miharu goes down the cargo bay to launch the missiles manually, but the ignition of the missiles causes her to lose her balance and she falls out of the open hatch of the Gunperry to her death. Kai returns from battle a different man, vowing to end the conflict between the Federation and Zeon.
The White Base makes it to Jaburo, where Amuro meets Lt. Woody. He is shocked to learn that Matilda was actually engaged to him and they would have officially gotten married if she returned to Jaburo. The crew also receive promotions and new orders: they are to become a part of a new independent decoy unit that will launch into space to attack the Zeon fortress of Solomon. Sleggar Law is also transferred into the White Base crew as a pilot. Zeon forces start staging an attack on Jaburo to stop the White Base from launching into space and use it as a distraction to set up explosives on the mass-produced Gundam hanger and the White Base. The White Base orphan trio, after finding out they were to stay in Jaburo and leave the White Base, run away and randomly stumble upon the Zeon men setting up the bombs. Despite being tied up and gagged by the Zeon soldiers, they manage to break free. Amuro, whose newtype abilities sense something wrong, finds the three orphans driving a car with all the explosives from the hanger in an effort to ditch the car before it explodes. With the help of Kai and Hayato Kobayashi, Amuro rescues the orphans and takes over the bomb-filled car, ditching it just before all the bombs detonated. Sayla, who was also searching for the orphans, stumbles upon Char once again, but their reunion is cut short after Char is spotted by Mirai. The attack escalates with Char joining the battle in his custom Z'Gok and Woody gives his life to protect the White Base Matilda cherished. The Federation Jaburo forces hold off the Zeon attack and the White Base launches into space, bringing the war back to Zeon.
Back in space, they are attacked by Zeon forces once again led by Dren. Amuro's newtype and piloting skills have gotten even better since his return to space, and he is now able to charge in behind enemy lines and take out battleships on his own, effectively obliterating Dren's fleet. This allows the rest of the pilots to focus on defending the White Base. After the battle, Bright decides to stop by the neutral colony of Side 6 to distract Zeon pursuers and not give away their intention to attack Solomon. Although Side 6 is a neutral colony, it is filled with many problems of its own. Bright cannot resupply weapons due to the neutrality of Side 6, Mirai is awkwardly reunited to her fiance, Cameron, and Amuro finds out his father survived the Side 7 devastation from the beginning of the series and is living in Side 6, only to find out that he has gone mad from oxygen deprivation. However, Amuro, taking shelter from rain, has a fateful encounter with Lalah. Later he would meet her again, except this time, he meets Char in person as well. Zeon fleets close in on Side 6, waiting for the White Base to leave the colony so that they can open fire on them, but Cameron offers to escort them to outside Side 6 airspace to make sure no fighting occurs before they are officially outside Side 6 boundaries. The battle inevitably breaks out once the White Base leaves Side 6 airspace, and they quickly destroy the Zeon fleets waiting for them.
Now on the way to Solomon, the White Base stumbles upon an abandoned Texas Colony, which was actually being used by the Zeon. Bright finds its presence suspicious and sends Amuro inside to investigate. There he finds Char in his customized Gelgoog and during the fight between the two, Lalah finds out that Amuro is the pilot of the Gundam. Detecting explosions, Bright sends in other crew members, including Sayla, inside the colony in cars to search for Amuro. Sayla finds Char fleeing the colony, but Bright unintentionally overhears their conversation through the buggy's comm unit waiting for news of Amuro. He learns the shocking truth behind the nature of Zeon and the relationship Sayla and Char share as the children of the late Zeon Daikun. Kai stumbles on a briefcase of gold and a letter addressed to Sayla convincing her to leave the White Base. Kai keeps this a secret from the other crew and Bright confronts Sayla about her relationship with Char and her loyalty to the White Base crew.
Shortly after, the Federation offensive on Solomon begins and the White Base meets up with them just in time to have a share of the glory. Zeon forces realize their chances of winning are slim, and Dozle Zabi, the commander at Solomon, sorties out in the mega mobile armor Big Zam to buy time for his family and troops to escape. Sleggar Law proposes to Mirai before the battle, but ends up giving his life for a chance for Amuro to close in and destroy the Big Zam since the Big Zam's I-field rendered all beam projectile attacks to be ineffective.
Now with Solomon under Federation control, the Zeon forces are quickly losing ground in space. However, Kycilia's newtype troops, led by Char himself, wreck havoc upon Federation ships stationed in Solomon through Lalah's Elmeth mobile armor and guerrilla warfare. Sayla during this time personally talks to Bright about her background and how she has lost faith in her brother she no longer knows. She then tells Bright to share the gold she received from Char among the members of the White Base and that she will not abandon the White Base now when they need her most. Char at the meantime, also reveals his identity to Kycilia, realizing that she knows about it and swears to remain loyal to her despite his blatant scheme to let Garma die. Kycilia and Char launch another attack at Solomon, and during the battle Amuro has his first newtype resonance with Lalah. Char, realizing that Lalah is being distracted, fights Amuro. Sayla also comes to support Amuro, and the siblings end up fighting each other. Char, after realizing that the Core Booster's pilot was Sayla through Lalah's newtype powers, stops attacking and exposes himself to Amuro. Amuro attempts to land a killing blow, but Lalah blocks it and dies. This event would leave both Char and Amuro traumatized for the rest of their lives.
Degwin Zabi, the head of the Principality of Zeon, attempts to arrange a meeting to discuss peace with General Revil. However, Ghiren Zabi, his ambitious son, arranges a Solar Ray System to fire upon them, also effectively taking out half the Federation fleet in the process and making himself the next leader of Zeon in the process. He then rallies the remaining military strength to the last remaining space fortress at A Baoa Qu for a final stand. The grand battle becomes chaotic as Char sorties out in the incomplete mobile armor Zeong, and the White Base and Gundam suffer heavy damage. Bright orders a crash landing and the crew now desperately fight off swarming Zeon mobile suits and soldiers now that the White Base has become a sitting duck. Meanwhile, Amuro and Char have an all-out fight in their heavily beaten mobile suits, both consumed by the rage from Lalah's death. Kycilia, realizing that Ghiren has abused his power, kills him, arranges a surrender for Zeon troops, and attempts to escape. Kai and Hayato's Guncannons are shot down and both are forced to flee. Char and Amuro take their fight to the next level, ditching their mobile suits to fight each other with firearms and even swords. Amuro manages to land a blow onto Char's head and Amuro arm is impaled. Sayla manages to find the two and stop them from fighting. Sayla and Amuro now make their way out of the exploding A Baoa Qu while Char stays behind to kill the fleeing Kycilia, continuing his vendetta on the Zabi family. When all hope seemed to be lost for Amuro and Sayla, both split from each other and wandering through A Baoa Qu, Lalah's spirit tells Amuro to use his powers to bring the survivors of the White Base together, ditch the White Base, and flee. As the White Base crew are fleeing from the explosion of A Baoa Qu, they witness the destruction of the White Base and they realize that Amuro isn't on their evacuation ship. Before anyone has the time to cry for Amuro, his Gundam's Core Fighter can be spotted in the distance and the all the survivors are finally reunited. Char also escapes with a handful of Zeon survivors. The surrender at A Baoa Qu results with an armistice between the Federation and Zeon. The One Year War has finally come to an end.