As the continuation of Zeta Gundam, this series once again follows the story of the Anti Earth Union Group (AEUG) battleship Argama after Zeta's final episode. To fight off the Axis Zeon, now called the Neo Zeon, Captain Bright Noa recruits a group of teenage junk collectors led by the loudmouthed but powerful Newtype Judau Ashta to pilot the Argama's mobile suits. Now sporting a line up of the behemoth MSZ-010 Double Zeta Gundam and the returning MSZ-006 Zeta Gundam, RX-178 Gundam Mk-II and Gundam-like MSN-00100 Hyaku Shiki, the group is nicknamed the Gundam Team. As such, this became the first of a number of Gundam series where a team of Gundam mobile suits fight alongside each other regularly. The climax takes place at Side 3 in the Battle of Axis. Out of the major Zeta Gundam characters, only recurring captain Bright Noa and Axis leader Haman Karn make more than cameo appearances in ZZ; Char Aznable's planned appearance was canceled when Tomino was given the go-ahead to do the Mobile Suit Gundam: Char's Counterattack movie. Yoshiyuki Tomino's original plan for the show which involved Char's return was neither revealed though Glemy's sudden change in motivation seems to give a hint that he fills in for him at the end, nor does Tomino himself remember it and aside from the openings, Amuro Ray does not make an appearance in the series either. The alternate ending presented in Mobile Suit Zeta Gundam: A New Translation retcons the UC Gundam Universe, possibly eliminating the events of ZZ Gundam.
Launching in the Double Zeta, Ple manages to drive off the enemy from the Argama, but now the federal forces are demanding that they disarm. When they hear from Fa that Kamille has disappeared, the Argama's crew divide up to help her search for him. While this is happening, Ple sorties alone in the Mk-II and finds herself in a tight spot. But then she hears someone's voice...
Hoping that a one-on-one battle with Haman will end the conflict, Judau launches in the Double Zeta. Haman too flies out to meet him alone in her white Qubeley. In the face of the Qubeley's furious assault, Judau's back is pushed to the wall. But protected by the wills of many people, he rises to face Haman.
Ple spots Judau's crashed core fighter, which is carrying an injured Leina. Judau leaves Leina with Ple and flies back out into the battlefield in order to save his friends. But Ple wants Judau to love her and her alone, and hates Leina with a passion. One that's strong enough to kill.
In shock over not knowing whether his little sister is alive or dead, Judau falls into a depression. Worried to see Judau in such a state, Roux takes it upon herself to administer some tough love. Just then, the Karaba base at El Goléa is attacked. Beecha and Mondo move to assist it, but misunderstanding Roux's motives, use her as a shield.
Now so angry with the Argama that she's deserted, Roux enters the free-trade city of Galdaaya, where an artist named June proceeds to hit on her. Meanwhile, while wandering the desert, Glemy is rescued by the "Blue Unit" of the African Independence Front, who coerce him into being a spy sent to Galdaaya's underground city. There he meets Roux.
Judau and the others infiltrate the docked mining asteroid Cicero in Core 3 sector. There they find Chara Soon commanding the workers. Although they join in a nascent revolt, the workers still don't entirely trust Judau. At the same time, Ple Two enters Cicero as well.
Pressing on with her plan for rule through terror, Haman makes the decision to drop a colony. Receiving a message from Hayato aboard the Audhumla, the Argama joins with the Karaba and heads to Dublin to begin an evacuation. However, the Karaba rescue of the evacuees is interrupted when they're attacked by a mobile suit unit led by Rakan Dahkaran.
Glemy plays his trump card and sends his Newtype unit into battle. He then makes to smash Axis's asteroid Moussa into Haman's fleet. Judau chases the now mentally unstable Ple Two into Axis and confronts both Glemy and Ple Two in the Queen Mansa.
Eager for a victory, Glemy awakens Ple Two from cold sleep in order to destroy the Argama. Sensing the evil presence of the Psyco Gundam Mk-II drawing near, Ple boards the half-disassembled Qubeley Mk-II to intercept it. However, she finds that both she and the mysterious pilot are able to anticipate each other's attacks perfectly...
Searching for Roux, Judau and the others enter Galdaaya, where they run into Glemy, whom is now leading Blue Unit. Just then, August, who is commanding the Mindra, strikes a deal with Gadeb Jasin of the African Independence Front to attack and seize Galdaaya.
The Neo Zeon forces move in to put down the Cicero uprising. Ple Two moves out, having received orders from Glemy to assassinate Haman Karn. However, she lets the captive Lucina escape. A change has come over her personality. Judau rescues Elle and the others from Haman's mansion, then confronts Ple Two in the Qubeley Mk-II.
The final battle begins between Haman's forces with Mashymre and Glemy's. The Nahel Argama, taking this chance to first strike at Glemy, launches the Gundam team. Amidst the free-for-all, Mashymre in a Zaku III Custom loses control of his overenhanced mental powers and is lost to the stars.
The Neo Zeon occupiers in Dakar invite people from the Earth Federation to a grand party they're throwing. Among them is Leina, brought there by Glemy. Taking advantage of the Gundam team's attack, Judau sneaks into the reception hall and finally gets his heart's desire when he's reunited with Leina. But...
With the Neo Zeon forces now in control of Dakar, Judau slips away from the Argama after it makes a water landing in the south seas, and meets Taman and his sister Anu. Taman takes a large sum of money from the Neo Zeon in exchange for attacking the Argama with the aquatic mobile suit Capule. Anu worries about what her brother is about to do.
The Argama rendezvouses with the Gundam team and sets course for Dublin. Bright heads off on his own for an interview with a federation high official at the Beech estate, but is followed by Judau. When Judau becomes violently angry with the official's lackadaisical response to the situation, he and Bright end up confined in the basement. They're saved from their predicament by Fa.
After sneaking into a meeting of the junk dealers association, Judau and his friends mistakenly signal that the ship can use the industrial airlock hatch to escape. Gemon and Yazan, piloting two Gezes, attack the Zeta Gundam, and the Endra has the Argama in its sights. But the hatch still isn't open...
Having finally departed Shangri-La, the Argama sets course for the La Vie En Rose. Chafing against Bright's command, Beecha and Mondo try to send a message that they're willing to sell out the Argama. Receiving their signal aboard the Endra, Mashymre sorties in the new mobile suit Hamma-Hamma.
Fa worries about Kamille, whom they left behind on the colony. Beecha and Mondo send another message, prompting Mashymre to send Gottn to try and infiltrate the Argama and make contact with these collaborators. Judau sorties in the Zeta Gundam, but his beam rifle is still unplugged...
Now a prisoner aboard the Argama, Gottn takes Iino hostage and escapes. Chara Soon attacks in the mobile suit R-Jarja. Just then, under Roux's guidance, the core fighter, Core Top, and Core Base begin to transform and combine. The new mobile suit Double Zeta Gundam is born!
Leaving the Argama on Earth, the crew returns to space in a shuttle to find the La Vie en Rose waiting with the new battleship Nahel Argama. But Judau and the others refuse when the kids are ordered off the ship. At that moment, they fall under surprise attack by Illia Pazom, a female soldier who has pledged her life to Mashymre.
Using the revolt against Haman to take control of Axis, Glemy battles Chara's fleet. Judau and Roux use the chance to sneak into Core 3 in order to kidnap Mineva, but fail. As the Nahel Argama appears to be supporting Haman's side, Ple Two approaches in the new mobile armor Queen Mansa.
At last, Judau Ashta is a member of the Argama crew. A team of three Gaza-Ds attack, but Judau is away negotiating with the junk dealers association for clearance to open an industrial airlock hatch. They're saved from this tight spot by a core fighter flown by a girl named Roux Louka from the La Vie En Rose.
Having taken Shinta hostage during the test of their improved main cannon, Chara steals the Core Top and flees the Argama. When Judau and the others fly out to intercept her, they find themselves facing Gottn in his new mobile suit AMX-008 Ga-Zowmn and a squad of Gaza-Cs. Judau attempts to try and retrieve the Core Top by forcibly docking his core fighter with it.
Torres agonizes over the knowledge that his old friend Cecilia is a spy for Gottn. Amidst the confusion of Chara's escape, Cecilia escapes on her own and goes to Gottn. Giving him phony information, she gets a ticket for an emigration ship. But the trunk supposedly containing her payment has a bomb set inside...
While the Argama holds position to cooperate with Karaba, the Gundam team receives orders to go on ahead to Dakar. As the team heads for a desert base, they find themselves under attack by the Rommel unit, who have been biding their time for eight years awaiting the restoration of the Zabi family. One by one, the Gundam team crushes the Rommel unit's old mobile suits...