The X-Men are aboard their plane, on the way to face Lucifer when a shaft of light appears out of nowhere, almost knocking the plane out of the air. When Xavier finally regains control of the jet, the team see that beam emanates from an opening in the sky itself. In this beam the X-Men see several strange objects flying towards a mountain.
The X-Men aren't the only ones who see this beam, a rancher named Mr. Mack also notices the strange light and he takes three men with him to investigate.
After the shaft of light vanishes, the X-Men fly towards the mountain, but erupting geysers prevent them from getting close. The professor is certain that the villain’s base is hidden in the mountain. Cyclops sees a suspicious river floating towards the mountain and then disappearing, apparently the water is needed to operate the geysers. Xavier decides to land the plane so that the team can investigate on foot, while the professor remains behind at the aircraft, following his students mentally.
Angel flies ahead when he is suddenly spotted by Mr. Mack and his three henchmen. Having heard about the X-Men robbing a bank in the news, they think the X-Men are evil, so they try to shoot down the Angel. Naturally Warren is too fast for them and evades the bullets.
As the ranchers try to pursuit the Angel they stumble upon the other X-Men and a small skirmish begins. Marvel Girl pulls Mr. Mack‘s hat over his eyes with her telekinetic powers and Cyclops scares them with a powerful blast. The four men fall into the river with their horses and while the three lackeys get out of there and head back to the town, Mr. Mack is persistent and tries to shoot Iceman with his pistol. He forgot all about Angel though, who dives from the skies towards him. He places him on his horse and Iceman makes an icecube around him, knowing that the horse knows the way home itself. With this danger solved the team focuses again on their business.
The river they spotted leads underground into the mountain, so Iceman makes an iceraft that the team can use to carry them into Lucifer's stronghold. When they are about to enter a large cave a whirlpool appears from below, breaking the raft apart and pulling the X-Men down.
Back at the landing site, the professor loses mental contact with the X-Men upon them entering the underground tunnel. By concentrating his mental power Xavier hopes to locate them, but he fails to notice two large robots sneaking up on him from behind. They quickly place a metal band around him so he can't move and they are immune to Xavier’s mental blast. The two robots take Xavier prisoner and fly off towards Lucifer's base.
The professor is taken to Lucifer, who explains his plan to enslave the world with and shows the professor his indestructible Dominus machine. The professor says the X-Men will stop him, but Lucifer isn't impressed and points to a large visi-screen.
The Angel has managed to escape from the whirlpool, but as the others might need his help, he dives into the whirlpool after them. Once down, he finds himself into an subterranean cavern and he spots Scott hanging on a pipe while holding Jean in his arms. He helps Scott and Jean to the shore of the underground river. The three of them go looking for the missing Beast and Iceman and see an opening in the wall. As they step through this opening suddenly a transparent cage erupts around them, trapping them.
Meanwhile the Beast is about to drown but then he gets pulled out by one of Lucifer's robots. The Iceman appears who saved himself on a surfboard made of ice and he slams straight into the robot from behind, freeing Beast. Iceman and Beast manage to take down the two robots and then leave but as they leave a metal wall suddenly appears in front of them and they slam into this wall, knocking them unconscious.
In the heart of the underground complex, the entire events were displayed on the visi-screen. Lucifer continues to tell the professor about his alien race who built the Dominus device. The machine is a very powerful weapon that can take away the independent will from entire populations. Dominus is so complex that it can only be operated by special robots.
The professor doesn't believe Lucifer, so he is shown images of their last conquest, a planet of the Sirius star. Dominus and the robots were sent to this planet through a beam of ionic light and after setting up a base of operations they completely enslaved the planet. Lucifer’s race have conquered many planets before and now Earth will be next.
Elsewhere in the complex, Jean, Scott and Angel try to free themselves from the glass prison but they fail. Three of the robots appear with the unconscious Hank and Iceman. As the robots are about to place them inside the same prison, which is called a “cosmic-cristalline cube“, the three X-Men in the cube plan to jump out of it as soon as the robots open the cube. Yet one of the robots activates a forcefield that holds the X-Men inside the cube, ruining their plans. With all of the X-Men trapped inside the cube, two of the robots leave.
Hank and Bobby slowly regain their consciousness, while the robot that was left behind starts to move the cube to a new location. Seeing a control panel on the wall, the Beast has a plan to escape. He lets Jean focus her powers on the lever that opens the cube and the X-Men manage to escape. The single robot is taken by surprise shot in the back of Cyclops‘ optic blast. The X-Men are free again and set out to find Lucifer.
As the X-Men escape, an alarm sounds and Lucifer orders his robots to search for the X-Men and destroy them. The X-Men are running through the enormous underground complex when two robots fly by. The X-Men hide and then they receive a telepathic message from the professor who tells them to not attack the machine called Dominus under any circumstances. When Angel discovers a passage towards the heart of Dominus a little dispute starts between Angel and Cyclops since Angel doesn't believe the telepathic message was really from the professor, so he wants to destroy the machine while they still have the chance. The others agree with Warren and they head deeper into the complex until the reach the core where they see Xavier and Lucifer.
The X-Men quickly come to the conclusion that the professor is under Lucifer's mental control since he isn't moving. As Lucifer reaches for a weapon, Jean uses her power to lift Lucifer's cape over his head making sure he can't shout any commands to his robots.
Angel flies towards Dominus, intending to destroy it. Cyclops wants Angel to stop but as he doesn’t listen which he uses his optic blast to shoot Warren down. Iceman agrees with Angel and throws a large rock of ice towards the machine, but Jean deflects it telekinetically. The X-Men continue to argue among each other whether the telepathic message really came from Xavier and if they should or shouldn't destroy the machine when suddenly the robots arrive.
As one of the five remaining robots flies towards Beast, he quickly leaps aside and the robot smashes into the
machine. The X-Men then see what the professor was warning them for. The robot that flew into the machine was completely destroyed while the machine itself was unharmed. The second robot dives towards the wounded Angel when Cyclops blasts the robot just in time. The last three robots them fly in formation towards the X-Men while firing rays at them. Iceman quickly conjures a curved shield of ice that deflects the rays at the machine. As these rays hit Dominus the rays are immediately backfired to the robots, destroying them at once.
As Lucifer curses the X-Men about destroying their robots the giant screen behind him lights up and his superior, the Supreme One, appears. Lucifer asks for mercy for his failure but the Supreme One is too upset with him since Dominus is useless without the robots to operate it. The shaft of ionic light appears again, drawing Dominus into it back to the aliens world.
The X-Men watch on as Lucifer fades into nothingness. As Dominus is completely gone the professor explains the X-Men that he probed the machine and learned that Dominus had the power to resist any form of attack, hurling back any force that tried to hurt it. This is why the professor wanted the X-Men to focus on the robots instead of the machine since the machine is useless without the robots. Having saved the planet once more, the X-Men return home.