The Thing is piloting a small spacecraft to Mars. In the back are Father Jennifer and December, Twilight and Smith of X-Nation in stasis tubes. The rocket is hit by cosmic rays and Ben radios mayday to the Ares colony on Mars. He remembers the original spaceflight that turned him and his friends into the Fantastic Four and, like back then, his arms feel heavy and he is unable to move. The rocket crashes on the Martian surface, which is observed by a green-skinned figure. It enters the damaged shuttle and attaches strange devices to the stasis tubes. Then, it pulls the unconscious Thing away.
There is some activity at the Phalanx globe in Earth’s orbit. A hole forms, through which a capsule is fired down to earth. As it hits the atmosphere, it is recognized by the Wild Boyz, who watch till it vanishes in an area of mist. Trash wonders if they should tell the Big Boss about it, but Shiv tells him that he already knows. They are living in a boat colony and, right now, in the arena of the main ship, there is a fight between Dorian and a green, malleable monster. The crowd cheers and, in the noise, a person called Mist Dweller grabs an anti-grav cycle and escapes. As the Wild Boyz see him heading off, they board their boat to hunt him.
In the Savage Land, Xi’An and Metalhead welcome the latest arrivals who survived the flood. Immediately, they befriend a little girl named Madeline, but her father orders her to stay away from the “muties,“ making Eddie lose his temper. Before the situation gets out of hand, the Human Torch lands in their midst. Xi’an thought him to be at the town meeting, but Johnny laughs; he would not want to get involved in that political stuff. In the center building there is the aforementioned meeting taking place. Two unnamed humans, Morphine Somers, Spider-Man Miguel O’Hara, Cerebra of the X-Men and the Invisible Woman argue about the future. They know that leaders are needed, but they have different views on how to approach this and the daily problems are getting bigger with each arriving shipload of refugees. Later, Sue searches out her husband in the labs. He is lost in his work as usual, trying to set up electricity and flowing water for everyone. As he becomes aware of Sue, he asks when the meeting will take place, but she replies that he already missed it. He apologizes with so much to work on, but Sue wants to know if he still is searching for a way to get them home to their boy, Franklin.
Deep within the Savage Land’s jungles, two explorers named Mr. Hodge and Mr. Winn await for the rest of their expedition team; their task – to explore the swamps and think about ways to make them habitable. Bloodhawk is the first to arrive and, immediately, he and Hodge start an argument, Hodge not being to fond of having to work with mutants. Winn interrupts them as a purple creature approaches, but it’s only Willow, who couldn‘t resist morphing around. Hodge has enough of them, and starts to make preparations for the other expedition members to arrive. Not far away, La Lunatica leads Nostromo and Jade Ryuteki through the jungle. Nostromo doesn’t feel well but, as Jade tries to help, he panics, fearing to infect her with his techno-organic virus, should she touch him. A sabretooth attacks the trio, but Luna easily finishes off the animal and they continue their march.
Back at the city, called Last Refuge, Metalhead attempts to dig a hole, as the scanner registered a large amount of water down below. As he is having problems, Mademoiselle Strange opts to help and casts a spell. It’s a little bit over the top, creating a big crater, but the groundwater is now accessible. Later, she is meditating in a quiet corner, as the Ancient One appears. He is angry with her, she has acted without thinking and her spell had an unwanted side effect - he states that her arcane energies awakened an evil beyond comprehension.
On Mars, Father Jennifer, December and Twilight have awakened from their stasis and wonder what to do. They think that the Thing has gone ahead to find the Ares settlers, as suddenly an alarm sounds. It’s Smith’s stasis tube; he doesn’t wake up and the chamber is overheating. Examining the tube, Father Jennifer discovers the alien device to it and, although they have found the cause, they need to help Smith before he dies. December tries to use her freezing powers, but apparently her power is adjusted to Earth’s climate. She is unable to lower the temperature. Only Twilight has a chance to help. December orders her to turn back the time within the tube and, remembering the many people who died recently (Clarion, Sister Nick), Twilight is eager to succeed – and does. Smith comes out unharmed and the four space travelers leave the ship to search for the Thing. Again, they are watched by a green figure.
On the coast of the Savage Land is a booty hunter, waiting for anything of worth to be washed ashore. Uproar and Wulff do not tolerate this and dump him off in the ocean, as suddenly Wulff recognizes a familiar scent. A few feet off lies the Mist Dweller who, although weak and drained, managed to escape the Wild Boyz. He babbles about creatures in the mist and having to warn Richards, so the two mutants take him to the city, only to find out that his chest is infected with a techno-organic parasite. In the city, Spider-Man and Cerebra examine the poor guy. She telepathically eases his pain, but he dies, repeating the same words again and again. Miguel scans the technology and apparently it came from the planetoid in Earth’s orbit. Instead of bothering Mr. Fantastic, Spider-Man opts to investigate this city in the mists himself.
In the jungle, Willow lets Mr. Winn explain to her some of his technical devices, but actually she tries to find out if he too is a mutant hater like Hodge. As he comments about her being cute, she runs off happily, though Hodge dampens her joy again by saying that he doesn’t trust shapeshifters. She could pose as anyone she wants and he would never know. High above, Bloodhawk soars through the skies and finally spots the other three. He rushes down and grabs Jade for a flight through the clouds; she is the sole reason why he agreed to work in this expedition. Winn shows some great interest of his techno-organic limbs as Nostromo arrives, but more importantly right now is the reunion with Willow. Nostromo thought the rest of X-Nation dead (killed by Exodus) and is happy to hear about their survival, though Willow has some bad news as well. Transforming into Clarion, she says that one of them did not make it.
At the Last Refuge, Strange is called to the crater. The water at its bottom is no longer water but blood. She gets a little bit closer to investigate, but suddenly huge hands of rock form and pull her down. The eruptions cause some minor earthquakes around the city. Mr. Fantastic is concerned about the lab equipment and Metalhead and Krystalin use their powers to shield some bystanders. Cerebra senses an unnatural presence at the quake’s core, but a psychic backlash keeps her from moving. She would have been crushed by falling debris if not for the Human Torch. Xi’An helps some humans to get out trapped family members by disintegrating the debris, though not all are happy to rely on mutant help. Angered, Xi’An lashes out against one of the moron and, in a corner, Morphine Somers secretly smiles.
The shockwaves even register on the equipment of the expedition team and some technical devises shut down. Jade asks Nostromo to try and use his powers to jumpstart them again but, while he does, his powers freak out. Techno-organic tentacles sprout out of him and, as Winn tries to be of help, Hodge shouts that touching the mutant could be dangerous. Suddenly, the ground gives in and Hodge falls down. Bloodhawk dives after him and catches him before hitting the bottom. They take a closer look at the cave and see an alien spaceship.
The Mars team gets closer to the Ares base, as they become aware of a yard full of empty graves. Suddenly, laser cannons lift out of them and December tries to erect an ice-shield, but again fails. Instead, Smith uses his control over machinery and, apparently, he has far greater control over his powers in the different environment. Single-handedly, he causes all devices to stop firing and explode at once. Twilight, though calling him a show off, can’t help to be impressed. They move on and reach the Ares base, only to find themselves surrounded by people pointing guns at them.
Down on Earth, Spider-Man has boarded a boat, intending to find the city of mist. He has already reached the now submerged island of Sicily, as he hears some noises in the back of his boat. He checks and finds two blind passengers: Uproar and Wulff. He demands an explanation, but, before Wulff can tell him of his history with the Wild Boyz, they are detected by his former gang, who fires an ion cannon on the heroes‘ boat. After the explosion, torn pieces of Spider-Man’s costume float in the water.