It’s a typical afternoon in the Baxter Building, the Fantastic Four’s headquarter, which means that about anything can happen. The Thing is carrying a statue of himself, created by his girlfriend Alicia Master, who is walking next to him. She hopes that the statue she carved does Ben justice, as she is blind and has to work by touch alone. The Thing, in his usual joking mood, says it ain’t bad, but no statue could be as loveable as he really is in living color. Meanwhile, Reed and Sue are reading a newspaper article about the X-Men. They find it amazing how famous they have become in such short time. The Thing interrupts, saying that they are no big deal. Who’d they ever lick? Magneto, the Space Phantom, the Blob, Quicksilver, the Scarlet Witch, Sue answers and Reed adds the Toad and Mastermind to her list. Ben gets the idea and shuts up. Johnny says that they forgot one – the Barracuda, whom he and Iceman recently fought together.
Having placed the statue at its intended location, the Thing complains that they all sound like a bunch of hero-worshippers. Once more admiring his girlfriends’ work, he tells Alicia that she is a better sculptor than the Puppet Master ever was. That or she just had a great model. Alicia sighs. She had hoped to never hear that name again. Realizing his mistake, Ben comforts Alicia and apologizes; he simply forgot that the Puppet Master is her stepfather. It was not his intention to upset her. Alicia tells him not to worry about it, but, gazing out of the window, the Thing knows how hurt inside she is. The Puppet Master better not come into her life again, or he’ll have to deal with him first.
However, exactly at that moment, the Puppet Master arrives in a secret hideout, exactly 12 seconds before his appointment, just like the Thinker predicted. The Puppet Master declares, right from the start, that he received the Thinker’s message, but he has contacted the wrong man and he won’t help him. Stepping into the huge lab though, he becomes aware of a huge faceless, gray-skinned creature and asks who or what it is. The Thinker tells him that it is an artificially created Android, originally invented by Mr. Fantastic, but now obedient only to him. The Thinker goes on to explain that with his oversized brain and his complex computers, he can learn, predict and accomplish anything. That is how he tracked down the Puppet Master, who has been in hiding for months. Masters is startled by the fact that anyone can steal from the Fantastic Four. In the past, they always defeated him, but now ... The Thinker agrees. His brain, coupled with the Puppet Master’s strange power, will lead them to success.
He hands his new accomplice a lead-lined protective suit to shield him from radioactive poisoning and tells him to put it on, for he is about to make his greatest puppet ever! Masters, convinced by the Thinker’s confident words, does as told and enters a specially shielded lab. Inside, he finds a rough mold of a head and radioactive clay. From outside, the Thinker guides him over a microphone. He tells the Puppet Master that he has examined every fact he could learn about the X-Men and deduced the identity of their mysterious mentor – Professor X. He tells the Puppet Master to use the head as a model, while he will describe what he believes his body looks like. Once he is finished, Professor X will be in their thrall as none should be able to resist the radioactive clay. The Thinker marvels as the sculptor models his little puppet. Once it is finished, he tells him to concentrate like never before, and the Puppet Master gazes at his creation and starts projecting his commands.
Sitting in the office of his mansion in Westchester, Charles Xavier suddenly feels somebody trying to exercise mental control over him. Though his body is confined to a wheelchair, his mind is one of the most powerful on earth and, utilizing every ounce of his will power, the Professor resists. Far away, the Puppet Master feels that he is not responding and wonders if his puppet is faulty, but the Thinker expected this to happen and advises him to add another four and a third grams of clay – quickly! Carefully, the Puppet Master does as told and once more tries to use his power, but still feels Professor Xavier fighting back. He wonders what kind of man he is. In his office, Xavier holds his head in pain as he tries to fight back the pressure on his mind. He fears for his X-Men’s safety should his power be used by an evil force. Xavier resists with all his might, but – he can’t. The pressure is too great.
Now sitting calmly again, Xavier follows the commands of the two villains. Using his telepathy he calls out to his students, who immediately follow his orders and enter his office. Xavier tells them that he has a new mission for them, one which they have to perform without question. The X-Men are to find the Fantastic Four, trap them and destroy them. At first, the X-Men believe he is not serious, but from Xavier’s expression they can tell that it’s no joke. The Beast wonders why they have to fight the Fantastic Four; there is no logic to it. The Professor tells him that this is for him alone to decide. His telepathy allows him to hear the thoughts of others and thus he learned that the Fantastic Four plan world domination.
Minutes later, a late model jetcopter, carrying the X-Men, approaches the Baxter Building. As they land on the roof, Cyclops once more reminds the others of the Professor’s orders – they’ll have to get the Fantastic Four off guard by making them think this is just a peaceful visit. Stretching his head from a window below, Mr. Fantastic recognizes who the intruders are and switches off the security systems so that the fellow heroes can enter the building. Introductions are made and, soon, the members of the teams are chatting with each other. Marvel Girl and the Invisible Woman comment on each other’s beauty, while the Thing admires the Angel’s wingspan, wondering if his team feeds him bird food, earning him a “mind your manners” from Alicia.
Although he hates to do it, Cyclops baits the trap, just like Professor X ordered. Claiming that the X-Men have learned of an alien spaceship, he asks Reed if the Fantastic Four would like to join them in investigating it. However, the Four’s leader turns him down; he and the Torch are putting the finishing touches on a nose cone they are developing for the Air Force and they can’t leave now. Scott thinks to himself that this is exactly what the Thinker predicted Reed would say (see notes) and starts the next phase of their plan. Without warning, he releases one of his optic beams, blasting the nose cone off its rack. Reed and Johnny are still surprised, when Cyclops starts aiming at them. Stretching his body, Reed evades several of the deadly blasts, while the Torch uses his flame against Cyclops. However Scott projects a wide-screen force beam, repelling the Torch’s attack with ease.
In an adjacent room, Marvel Girl is trying to convince the Thing of the importance of accompanying them, however Ben replies that he is too busy admiring his favorite hero, namely Ben Grimm. Jean states that they must come with them, they have their orders, but the Thing doesn’t care. Marvel Girl then says that she will make him join them and telekinetically lifts the statue into the air. However, it is too heavy for her and it falls, breaking apart. She immediately apologizes, but Ben gets mad and exclaims that, if she weren’t a female, he’d demolish her. However, as it is, he can only give her the spanking of her life. Jean tells the Thing to stay away from her, once more stating that it was an accident. However, as he still approaches her, she uses her telekinesis to keep the Thing off-balance by spinning him around.
Having heard the commotion, Sue opens the door from yet another room and tells Marvel Girl to stop. However, Warren comes up from behind her and lifts her into the air. He tells the Invisible Girl not to struggle and make this any harder; they have their instructions. Sue warns him and the Iceman of what the rest of the Fantastic Four will do with them, but the two X-Men proceed with their plan and, while Bobby traps the female member of the Fantastic Four with an ice-lasso, the Angel gently puts her down again.
Back in the lab, the Beast has joined Cyclops in fighting the Torch and Mr. Fantastic. Reed tells Johnny to keep Cyclops busy, while he tackles with the agile X-Man. The Fantastic Four’s leader takes on the shape of a ball and attempts to roll the Beast out of the way, but the X-Man jumps on top of him and keeps his balance. Reed decides to take on another approach and, all of a sudden, unfolds his pliable body, causing the Beast to fall. Reed then grabs him and throws him towards a wall, but, by bouncing around, the Beast uses his momentum to his own advantage and again leaps towards Mr. Fantastic. Reed wonders what the X-Men’s motive is, as the battle goes on.
Reed evades Hank’s attack, who then hurls through the door into the Thing, who is still held in mid-air by Marvel Girl. She thanks her teammate for his assistance, as she could not hold the Thing off for much longer, but Hank explains that his arrival is purely by accident. Before Hank can get up, Ben grabs the red-haired X-Man, who cries out to the Beast to help her. The Thing punches at the Beast, but he is faster and leaps out of his reach. Still, he wonders how he can possibly hope to defeat him. Unexpected help arrives in the form of Iceman, who covers the Thing’s head, and then his feet, in blocks of ice. That should at least hold him off long enough for them to complete their mission, he thinks.
In the lab, Mr. Fantastic asks Cyclops not to use his power on the experimental ray machines, but Scott does anyway, as this seems to be the only way to force the Four into surrender. Johnny prepares to launch a huge fireball, but Reed tells him to stop as he has reached a decision. They have to learn the reason behind all of this, so he does as told and surrenders. Cyclops says this is a wise decision and, to assemble them all in the same room, he blasts at the Thing, who then slides on a frozen part of the floor. Right then, Ben smashes the ice-blocks that are trapping him and he is only too eager for a re-match, but his teammates calm him down. The next move is up to the X-Men.
The five mutants lock the lab door behind the three members of the Fantastic Four and then hurry with their plan. The Invisible Girl, still held by bonds of ice, is placed in a locker so that she can’t pull off any of her “invisibility tricks” on them, while the Angel flies out of the window to get the team’s jetcopter. Only seconds later, it hovers next to the window and the X-Men jump into it, Hank carrying the locker with Sue inside. They then head for Destination A, slow enough to make sure that the rest of the Fantastic Four can easily follow them.
Right after the mutants have left, the Thing breaks the lab door, freeing himself and his comrades. Johnny wonders why Reed can stay so calm as if he wasn’t worried about Sue and the leader of the team explains that he is, but doesn’t believe her to be in any real danger. Looking out of the window, they see the X-Men’s jetcopter depart and decide to follow them, even though that’s what the X-Men wanted them to do right from the start. The Thing finds Alicia sitting on a console and lifts her down. The blind sculptor is confused; somebody placed her there and she heard all that went on, but doesn’t understand. Reed takes this as proof that the X-Men meant no harm; they even put Alicia to safety. Ben tells his girlfriend to just stay there, where she’ll be okay, while they go after the X-Men.
Minutes later, Reed, Ben and Johnny are aboard the Fantastic Four’s pogo plane, following the X-Men’s trail with the plane’s radar computers. After Mr. Fantastic explains the device and all its functions, Ben Grimm points out that all he was actually saying was, “they went that way.” If Reed and the Beast would ever get in a real conversation, the Thing remarks, nobody would understand them, except maybe Noah Webster. However, Reed says that Ben doesn’t fool them. He has a college degree or two himself. They knock off their banter when they see the X-Men’s jetcopter slowing for a landing. However, once they see where they landed, they wonder if they had engine trouble, as it is on top of a lonely plateau, with no way to escape. Whatever the case, they too descend.
Down below, the X-Men, with Sue Storm, have gotten out the craft, awaiting further orders from Professor X. The Invisible Girl is surprised. The mutants battled the Fantastic Four and kidnapped her without knowing why? The Angel explains to her that the one who guides them knows exactly what he is doing, just as Xavier’s mental transmission comes in. The X-Men are to battle the Fantastic Four again once they leave their plane and, this time, they have to completely subdue them. The X-Men asks the Professor for an explanation, but it’s no use, as he already broke the thought-connection.
Once the pogo plane has landed, battle ensues once more. Iceman and the Torch use their thermal powers on each other, the Invisible Girl traps Marvel Girl inside a forcefield, and the Angel evades Reed’s stretched limbs. Cyclops tries to keep the Thing at bay with his force beam, but, despite him blasting at full force, the Thing slowly gets closer. However, all of a sudden, a hole opens in the ground beneath Ben’s feet and he falls into a pit. Reed tries to rush to aid him and the Angel takes after him, trying to stop him. However, before Warren reaches Mr. Fantastic, a revolving reel device springs from the ground and spins Reed’s limbs around, stretching them to their limits. Seeing his lover in need, Sue decides to drop her forcefield around the telekinetic, a few seconds too early, as the Human Torch is also on the way to help him. Before any of the X-Men can even think of fighting them, another booby trap is activated. Two capsules are ejected and upon hitting brother and sister, which release some sort of asbestos-covered straightjackets, effectively trapping them. As they fall to the ground, no longer capable of movement, Sue once more questions why the X-Men even fight them.
While the confused X-Men ask themselves the same question and also wonder who booby-trapped the plateau, a large section of the earth suddenly lifts aside, revealing an underground complex. The Thinker, the Puppet Master and the Android emerge out of the secret access. The mutants recognize them from newspaper articles about the Fantastic Four defeating them. However now, the Thinker points out, it is they who have won, using the X-Men as the bait. The Puppet Master gloats that as long as he has Professor X under his control, the X-Men will obey them. Cyclops finally understands that they are responsible for Xavier’s strange commands.
Once more manipulating the puppet in his hands, the Puppet Master orders Professor X to put his team sleep. Many miles away, Xavier responds and uses his telepathy to render his students unconscious. But as great as his brain power is, when spread over five subjects at once, it is diffused, thinned out to the point where another strong mind might resist – a brain like that of the Beast. Hank only fakes unconsciousness and sinks to the ground among his teammates, but then swiftly jumps upon the Puppet Master, wresting the doll from his hand and crushing it under his foot. The villain cries out in despair, as he sees his greatest creation so far destroyed beyond repair. He doesn’t want to be defeated again.
Meanwhile, a few feet below the ground, Ben Grimm has no idea of the events transpiring on the surface, but he has no intention of staying in his prison longer than he has to. He punches himself stepping holes in the walls and climbs up. As he reaches the plateau again, he first becomes aware of Reed and helps him untie the many knots the reeling device put into his body. After the initial help from the Thing, Mr. Fantastic can free himself and he tells his friend that they need to help the X-Men. Naturally, the Thing is confused, but Reed explains while they tear the coverings of Sue and Johnny. Now reunited, the Fantastic Four rush over to the X-Men, who are fighting the Android. With the puppet destroyed, the Android is the villains’ last line of defense. The Thinker announces that the creature follows his every command and can defeat an entire army. The heroes haven’t got a chance.
The Human Torch flies over to Iceman, who has covered one of the Android’s arms with ice. Johnny warns him that the Android can take on the characteristics of whoever attacks him, but it’s already too late and the creature encases the Torch in a block of ice, knocking him out of the air. Hitting the ground, the ice breaks open – Johnny is unhurt, save his pride.
Marvel Girl tries to lift the Android with her telekinesis, but it’s too much for her, so Cyclops helps with his optic beam, knocking the Android over. Sue warns them that it is indestructible and tries to contain the Android in her forcefield until they can think of a better solution. However, the creature is too strong and breaks free. The Thing takes this as his cue and starts to fight. In vain, Reed tries to warn him of the Android powers, but, not before long, Ben learns it the hard way, as an oversized, scaly fist punches him in the face.
Back in Westchester, Professor Xavier finds himself released from the Puppet Master’s spell. Announcing that whoever is responsible for what has happened will find that there is no place on Earth where he can hide from his vengeance, Xavier sends out his thought waves, grasping the entire situation on the plateau in a fleeting instant. The Professor discovers that only one thing will stop the Android – a precise pressure to the exact control center of its artificial body. Xavier concentrates and, from many miles away, applies mental pressure to exactly this spot and the Android is deactivated.
The Thing once more has no idea what is going on. A few minutes ago he landed a blow, but that shouldn’t have been enough to drop the creature. Reed, of course, begins to suspect that this was the accomplished by some invisible command, a thought that struck out of nowhere. Cyclops tends to Jean, while the Angel wonders where the two villains are. Last he saw, Iceman says, the Beast was chasing them into the big complex. The two X-men prepare to go after their comrade, but a mental command from Xavier tells them that it is already too late. In a tunnel below, the Beast makes the same discovery, when a sliding door separates him from his prey.
On the other side of the steel wall, the two villains board a craft. The Puppet Master had no idea it was there, but the Thinker says he has always an alternate plan in case he should miscalculate. This time everything was perfect until he allowed the accursed puppet to be smashed. While the Puppet Master ponders their narrow defeat, the Thinker already thinks about the next challenge ahead. Then, his plan will be flawless. A hole opens in the mountainside and the craft flies away.
Up on the plateau, the heroes can only watch them leave, right as Hank returns from the complex. Iceman is sure that, sooner or later, they’ll get caught, while the Angel walks over to Mr. Fantastic and apologizes on behalf of his team. They have just been following orders. They had no idea the Puppet Master was behind them. Reed sys there is no need for any excuses; the X-Men were valiant foes and equally valiant allies - the Fantastic Four are proud to have met them.
As the X-Men depart in their jetcopter, the Fantastic Four discuss them. Reed thinks they are a wonderful group and they will be great heroes, while Sue wonders who they really are underneath the masks. The Thing, meanwhile, just calls them a freakshow. Reed then turns to the fallen Android, saying that if it was beaten in the way he suspects, the X-Men’s leader is a far wiser man than anyone dreams. Johnny thinks it strange that they had to fight one of Reed’s creations and Mr. Fantastic explains that this is the irony of science; no invention is good or bad by itself, it's only the use to which mankind puts it that really matters. As the Fantastic Four prepare to return home, they wonder whether they’ll meet the X-Men again.