Jump Force: Age of Father, the epic follow-up to the biggest anime movie of all time. When Edward Elric tries to jumpstart a dormant peacekeeping program, things go awry and Earth’s Mightiest Heroes, including Edward Elric, Sorey, Son Goku, Naruto Uzumaki, Akame, and Sebastian Michealis, along with support from Ciel Phantomhive and Zombina are put to the ultimate test as the fate of the planet hangs in the balance. As the villainous Father emerges, it is up to the Jump Force to stop him from enacting his terrible plans, and soon uneasy alliances and unexpected action pave the way for an epic and unique global adventure.
A year has passed since M.O.N. collapsed with the reemergence of the terrorist organization CCG. With M.O.N. no longer heading their operations, the Jump Force reassemble for the first time in three years to track down and eliminate CCG cells themselves, using Edward Elric's resources to help.
Their latest mission brings them to the location of the Dragon Ball that Vegeta utilized during the Hollow Invasion; the Dragon Ball is now in the possession of Arima, one of the notorious heads of the CCG who has been using energy drawn from the Dragon Ball to power advanced weaponry, as well as attempting to empower living beings. A raid on Arima's base in the Eastern country of Hellawes commences, with the Jump Force battling CCG forces to reclaim the Dragon Ball. During the battle, without Arima's approval, two of his agents join the fray: Issei Hyoudo and Rias Gremory, demon lovers who are the only ones to have survived exposure to the Dragon Ball's energy, and have gained boosts to their already supernatural powers as a result. Issei is bound to a dragon spirit called Drege allowing him to use the Boosted Gear, while Rias possesses a powerful plethora of magical powers. The lovers are able to hold their own against the Jump Force, but are unable to prevent the heroes from capturing Arima. Edward finds the Dragon Ball, and Rias attempts to stop him by using her powers to implant a vision into his mind. In his vision, Edward sees his teammates dead while the Hollow launch an even larger invasion on Earth. Upon seeing Edward's nightmare, Rias suspiciously allows him and the Jump Force to take the Dragon Ball away before fleeing with her lover.
With Arima arrest, the CCG has suffered a great blow and the organization is left in a state of discord. Returning to Elric Tower with the Dragon Ball, Edward and Naruto Uzumaki begin studying the Dragon Ball. Their research leads to the discovery of a net of neurons that, according to Edward, could be reconfigured into an artificial intelligence stored inside the Dragon Ball. The two extract it for use in Edward's secret peacekeeping program – "Father" – designed to allow the Fullmetal Legion to operate independently and safeguard Earth under the direction of an advanced Homonculous. After three days, the project is seemingly met with little success. However, while the Jump Force throw a party to celebrate their recent victories, Father suddenly activates. Somehow already self-aware despite Edward's alchemy having not made it that far ahead, Father immediately determines that the only way to save Earth is to eradicate humanity, which he deems as the prime factor in the planet's turmoils.
Using a Fullmetal Legion armor, Father uses human transmutation to make himself a crude, black mass covered in eyes and mouths for a temporary body. After the Jump Force have finished their party, the team, joined by Zombina, Roy Mustang, and scientist Makise Kurisu hold a small contest to see who can beat Goku in an arm wrestling contest. Their contest is interrupted when Father suddenly directs the Fullmetal Legion to attack them, and an intense battle ensues. During that battle, Father has a chance to kill Makise, but mysteriously spares her life. While most of the Fullmetal Legion is destroyed by the Jump Force, one armor manages to escape with the Dragon Ball and flees to the Hellawes CCG base, where Father uses the CCG technology stored there plus his innate knowledge of alchemy thanks to being a Homonculous to begin construction of an army of Fullmetal Drones as well as his own more refined body.
After the battle, the team confronts Edward about his secrecy, while Father recruits Issei and Rias, who have a vendetta against Edward because an Elric Industries alchemy bomb killed their friends; Rias had willingly allowed Edward to make off with the Dragon Ball with hopes that his fear of letting the world die would lead to him constructing his own undoing, which in this case appears to be Father. After Father kills Arima to lure the Jump Force out, he and the demon lovers travel to South Africa to acquire Quinke Metal from arms dealer and Fallen Angel Azazel. The Jump Force try to stop them, but Rias hypnotizes Goku, Akame and Sorey, giving them vivid hallucinations that render them invalid. She then hypnotizes Naruto, turning him into a semi-complete chakra created body of the Nine-Tailed Fox and sending him to attack a nearby town. Edward decides to call in "Alphonse," which deploys the Fullmetal Armor MKV, a larger suit of Alphonse's armor designed for when/if Edward needed to defeat the Nine-Tailed Fox, but the destruction they cause starts a public backlash against the Jump Force, who are forced to go into hiding.
The team takes refuge at Phantomhive Vacation Home, where they meet Ciel's other servants and Sebastian's underlings. Having experienced apocalyptic visions in his hallucination, Goku leaves, traveling to the mystical "World of the Kais" to determine the meaning of his hallucination. Akame and Naruto plan to run away and start a new life together when Father is defeated. Ciel Phantomhive arrives at the homestead and encourages the Jump Force to form a plan to stop Father. Naruto deduces that Father is planning to create another body made of synthetic tissue, using the "Dragon Transmutation" device developed by Dr. Makise Kurisu.
Meanwhile, Father, Issei and Rias go to Makise's laboratory in Japan, where Father reveals his plan to use the Quinke Metal samples in conjunction with Makise's synthetic tissue generating "Dragon Transmutation" device to create a more powerful body for himself, with the Dragon Ball as its primary power source. To ensure her cooperation, Father takes control of Makise's mind with the Dragon Ball. As Father transfers his consciousness into the synthetic body and Makise implants the Dragon Ball into its chest, Rias curiously looks into Father's mind and discovers his plan to destroy humanity. Horrified, the lovers turn against Father, who leaves the laboratory with the "Dragon Transmutation Device." Arriving in Japan, Sorey, Akame and Sebastian battle Father, who kidnaps Akame and derails a train to slow the Jump Force down. Issei and Rias aid Sorey in rescuing passengers from the train, while Sebastian retrieves the "Dragon Transmutation Device" and takes it back to Elric Tower.
At Elric Tower, Edward and Naruto use the Philosophers Stone to perform human transmutation on the synthetic body as an attempt to rectify their mistake with Father. Believing Edward is about to potentially create another Father, Sorey, Issei, and Rias try to stop them, but Goku arrives and brings the body to life with ki from his Super Saiyan Blue transformation. The resulting being thankfully proves friendly. Goku explains that the Dragon Ball – one of seven, the most powerful objects in existence – which Goku saw in his hallucination, and its power could be advantageous against Father. Issei, Rias, and the synthetic Homonculous, who is later given the name "Greed", ally themselves with the Jump Force, who return to Hellawes to end Father's threat once and for all.
Arriving in Hellawes, the Jump Force find that Father has used the remaining Quinke Metal samples and Hollow anti-gravity technologies being studied in the CCG facility to build a machine that lifts a large part of Mt. Killaraus, the Hellawes volcano plus the small town nearby, into the sky. His intent is to crash it into the ground to replicate a meteor strike, causing a mass extinction event. While Naruto rescues Akame, the Jump Force evacuate civilians from the town and fight Father's army of Fullmetal Drones, but they are unable to evacuate everyone before the volcano begins to ascend. Ciel and the revived M.O.N., joined by Roy Mustang, arrive in a Helicarrier to assist in evacuating the last few civilians. Akame and Naruto, now transformed into a more refined Nine-Tails form called "Chakra Mode", enter the fray and the team converges on the location of Father's device. There, they wipe out most of Father's drones and severely damage Father's primary body. In retaliation, Father hijacks the Jump Force's jet and kills Issei. Naruto leaps into the jet and tosses Father to the ground, where a grieving Rias finds and destroys him.
One of Father's drones deactivates the device, causing Mt. Killaraus to begin plummeting towards the Earth, and forcing the other Jump Force members to flee aboard the Helicarrier alongside the evacuated citizens. Meanwhile, Edward alchemizes the volcano and Goku, in Super Saiyan Blue form, uses a Kamehameha to reflect off the core. The ensuing explosion shatters the volcano into rubble, which falls safely into a nearby lake. Naruto, seeking peace after the battle, gets Akame to safety and departs in the jet. Father's consciousness attempts to flee in the last remaining drone, but Greed confronts him. The two have a brief exchange of ideals before Greed obliterates the drone, effectively ending Father's threat.
The Jump Force establish a new base in Amestria, run by Ciel, Makise, Zombina and Dr. Briefs. Akame assumes Naruto is dead because the jet cannot be tracked, and silently mourns for him, but Ciel assures her that he is likely still alive. Believing the Dragon Ball is safe with Greed, Goku returns to Planet Vegeta to learn more about the Dragon Balls, while Sebastian and Edward also leave the team. Sorey and Akame assemble a new Jump Force team, consisting of Rias, Zavied, Mustang and Greed.
Meanwhile, Omega Shenron retrieves a Dragon Ball saying "Fine, I'll do it myself." and then begins his hunt for the remaining Dragon Balls.