The Junior Elite stood in the lab of Magnificent Man, Xion unconscious on the floor and robot-butler Symba having gone full berserk mode. Black Hoodie, with support, hacked into Symba and forced an emergency shutdown. Symba was locked up, and Xion explained that as he was constructing a possible gateway to bring back The Elite, a presence entered our dimension and possessed Symba. Xion is convinced that the Elite are lost and wants to take apart the gateway his was building before something worse passes through.
At the same time, local Halcyon news is reporting the team’s visit to the Eon Institute as an illegal break-in and framing is as youth gone wild in the absence of their adult authority figures. Magnificent Lad is fed up with this, as it adds to his internal frustration over his search for his parents, so he rockets off to the site of the live news story. He shows up attempting to plead his case. Earlier, Gen. Juliet Mayhem of AEGIS cryptically warned him that certain forces would seek to weaken The Junior Elite through public perception. Mag Lad begins explaining what is going on when a powerful force bolts from the sky and carries the hero off in a bear hug.
On the television, the rest of the team sees Apollonia is the culprit. Apollonia is the alien queen, exiled to Earth and was one of the lost members of The Elite. She’s apparently under strict mind control. Kid Atomic gathers the team onto his Warthog, and they fly off to help Mag Lad. A battle ensues and using an extension of Black Hoodie’s psychic powers they wrest control of Apollonia’s mind back. The heroine is grateful to be free of the control and explains that she believes The Elite are lost to the Dark Dimension, now in the thrall of an omnipotent entity called Golgotha.
Gen. Mayhem gives Kid Atomic a lead, letting him know the mysterious overpowered weapons Professor Dark and his crew were wielding came from a lieutenant in the Fortunato crime family, Rocco di Chiara. The Junior Elite arrive at Di Chiara’s front, an Italian tailor’s shop in the Little Sicily district. They try to talk their way in with the elderly Italian tailor, but he catches on and unleashes the shop’s hyper hi-tech security system. Busting their way through the blast door and past the energy cannons and find a shipping center in the back where made men are prepping weapons for distribution throughout the city. Rocco shows up with some more men, armed with the interdimensional weapons and fires on the team as they try to escape, disrupting Silver Arm’s energy construct. The team plummets and Mag Lad barrels into Rocco, creating a crater in the street that brings the villain subterranean. Rocco gets off a lucky shot, incapacitating Mag Lad and he and his men escape.
Meanwhile, back in the Magnificent Island laboratory, Xion is busy dismantling the interdimensional gateway when a twisted, talon-like hand bursts forth and grab’s his, crushing the bones like paper….
Xion is missing, and the Mag Island lab is in disarray. The team got beaten badly by Rocco Di Chiara and his men and now Gen. Mayhem has shown up to tell them it’s time to give up the search for The Elite. Apollonia sides with Gen. Mayhem but the Junior Elite defiantly say they will find their mentors with or without their help. Kid Atomic begins searching for Xion and discovers traces of his blood on the floor, Gravinian blood, which is extremely rare to see because of their species’ impervious skin. There are also traces of interdimensional energy, energy from the Dark Dimension in the lab. The Sphinx uses her postcog powers to see a half a dozen alien soldiers emerge from the gateway and leave Xion a bloody mess. Once they were done with him, they spread out through Mag Island.
A check of the island’s security feed finds them in the hangar bay attempting to commandeer a Gravinian shuttlecraft. Black Hoodie hacks the island’s security systems and uses the Warthog’s atomic ray to make quick work of the alien cyborgs. They rush to hangar bay to make sure it’s secured, just in time to witness explosions going off on the AEGIS city skyship that was over Halcyon. Apparently, sleeper agents belonging to the cult of Golgotha were onboard and are bringing the ship down over the city to perform a mass blood sacrifice to their god. Mag Lad calls on some guardian drones that patrol Mag Island and they rocket off to steer the crashing ship to the waters off the coast. Kid Atomic, Silver Arm, and The Phoenix rode in the Warthog while Black Hoodie and The Sphinx took the Gravinian shuttle.
The crashing ship was dropped roughly in the bay, but the sleeper agents began a weaponized assault on the AEGIS agents who were losing ground due to still being in shock from the surprise attack. Silver Arms extends his constructs as tendrils to wrest the weapons from the sleepers but the air is cracked by a sonic boom and Magnificent Man comes flying down. However, he is transformed, turned into a twisted shadow version of himself. Acting quickly, Silver Arm unleashed a giant winged dire wolf that swallows Mag Man and hurtles into space to take the ultra-powered hero out of the action. The tide turns between AEGIS and the Golgothans, which allows the Junior Elite to pursue the wolf and Mag Man.
They find Mag Man shredding the wolf construct and then turning his rage back towards Silver Arm. Black Hoodie, her powers boosted with help from Kid Atomic, grabs Mag Man’s mind and lets Mag Lad speak to his father in an attempt to bring him back. Cracks form in the demonic hold, but Mag Man crashes himself into the moon as his mind and body go to war. Mag Lad talks his dad through it and destroys a device that seems to be phasing his father back and forth between this world and the dark dimension. When the device is damaged, Mag Man is back, but his powers are gone.
Returning to Halcyon, the Junior Elite finds a rift in space and time over the Eon Institute flooding more of the alien soldiers through. Also returning to action are Apollonia, Doctor Atomic temporarily recovered from his PTSD, and Mag Man piloting the Gravinan shuttle. They rush to Eon and muscle their way past Dr. Conway Claremont who wants to preserve the gateway in his lab. Waiting for the Junior Elite at the gateway is Gehenna, Golgotha’s second, with her pet, the twisted demonic version of adult Silver Arm. The Sphinx gazes back and sees the Gehenna uses a control rod to force adult Silver Arm to bend to her will. Junior Silver Arm unleashes his dire wolf construct again who pins Gehenna to the wall. The Phoenix wrests the control rod but she and her twins’ power go haywire due to the presence of the gateway. Multiple rifts in both time and reality are torn open. Through one of them, the team can see the young Phantom Spider, the man who would grow up to the guidance counselor at the high school. He can apparently see them and steps through the rift only to be killed by the manipulated adult Silver Arm. This pushes the team to return Gehenna and her soldiers through the rift and then destroying the gateway.
In the wake of this battle, a few things becomes apparent to The Junior Elite:
- Adult Silver Arm, like Mag Man, has lost his powers, the silver arm sloughing off as an inert shell
- Magnificent Woman and Vanity Fair are still lost
- Phoenix and The Sphinx encounter a being that exists outside of time and tells them the death of their mentor, Phantom Spider, outside the normal path of time is being added to a list of charges past, present, and future. He warns that one day they will be prosecuted for these time crimes, but for now, they are safe.