Spider-Man reviews with his classroom full of children the days lesson of time not being constant, matter being malleable and that gravity can be defied. He emphasizes this last point by dropping a fruit he is holding from his position of standing upside down on the ceiling. The fruit drops down from him and splats on the ground. Spider-Man concedes that “sometimes” gravity can be defied. As the school bell rings, he reminds the kids to read their chapters and tells them that they will be learning about Newton's law of universal gravitation by dropping things off the roof.
As he teaches, Spider-Man thinks about how, as a kid, he dreamed of going to the stars and saving the world. Now he dreams about being a nerdy kid whose biggest problem is being picked on at school. He dreams of living a normal life without radioactive spider powers or green goblins that throw his girlfriends off bridges. He thinks about how he has seen and done things that defy every law of physics, but he can never break the rule that says his life will always be an unbelievable challenge. He has always done his best to make the best of his situation and even laugh about it along the way. This man named Peter Parker is the last science teacher on Earth, and this is the end of the world. He stares out the window at a crowded residential district of a city with destroyed skyscrapers in the background. The students are dressed in modern day clothing and have modern devices like the iPod, yet they resemble apes as much as people, the Small Folk.
Walking into the locked teacher's lounge, Spider-Man thinks about the term papers he has to grade of these two dozen teenage ape creatures. He walks into what he calls the Dead Weapons Office and it is full of various devices and costume parts of past heroes. Captain America's shield, parts of Iron Man's armor, and Green Goblin weaponry are some of the visible gadgets. He asks the ape-man Mikal how things are coming, and Mikal responds that the diggers just dropped off another batch from Sector 17. When asked if any of it is promising, Mikal responds that all just looks like junk.
Spider-Man recalls that there was a time where you couldn't turn the corner without tripping over a new ultimate nullifier. Now they can't seem to find a single weapon of mass destruction on the entire planet. He looks over at a dormant cosmic cube and asks if there have been any changes to it. Mikal responds that it still looks like just a glass box and inquires as to what it was supposed to be. The cosmic cube could do pretty much anything, Spider-Man explains. Mikal says it’s too bad they can't figure out how to turn it on. Spider-Man refuses to give up hope on the cube, claiming that there is still some dormant energy in there. They are so close to maybe saving this world.
Suddenly, an alarm sounds and Spider-Man asks Mikal if that means what he think it means. Mikal says the only reason for the alarm to sound is if the spotters have seen something, and quickly grows concerned after looking through the telescope. Mikal rushes off to the temple as Spider-Man angrily realizes that the man who killed every single person on Earth has returned to take whatever is left of it. If only he had a few more weeks, he shouts, slamming his fists onto the table. He almost laughs at the irony of a man lost in the timestream needing more time.
Spider-Man swings through the ruins of the city observing the Small Folk returning to their loved ones. He thinks about how it would be nice if he had any loved ones left since as far as he can tell, everyone he has ever known is dead and he is the last human on Earth. Well almost the last he admits, though he uses the term human lightly with “him.” He still has no idea how he got to his place or why he is bouncing like a pinball through time. He doesn't know how to get back either but at least he cobbled together some web shooters and found a new costume. Passing a super hero wax museum, a statue of Spider-Man, missing its suit, is on display as one of History's Lamest Heroes. The costume has the word “lame” printed huge on his butt and he realizes that it really isn't like the old days, no matter how close it feels sometimes.
At a store called Elite Androids, Robots for Your Household, a gathering of Small Folk plead and pray for their Messiah to save them. The entrance is blocked by large signs claiming that trespassers will be stabbed repeatedly and that “This means you Parker!” Inside the building, Wolverine is cloaked in Samurai garb and wears his hair in a Samurai braid. He instructs the menacing-looking robots around him to override the alpha seventeen kay zero protocols. The machines warn him that this may prove hazardous to the user. Wolverine replies that is the idea and “snikts” out his claws.
After thoroughly trashing all the robots, he stands amid the scrap metal of their remains and speaks into the darkness. “Doesn't matter how many ways I say it, you'll never leave me alone... will you, Parker?” Spider-Man climbs down the wall and assures him that he would but then he would have to go back to teaching fifth grade hockey to get his regular dose of senseless violence and Canadian crotchetiness.
Wolverine claims to have heard the bells and knows why Peter is there. Peter is relieved that Logan knows how it must go from this point forward. According to Peter, after telling Logan the world is going to end, they will have a manly sleep over where they tell tales of adventure and in the morning they will march to their deaths like devoted brothers in arms. Logan knows that Peter hasn't found a weapon or he wouldn't be here. Well maybe Peter just loves their conversations, you know like ingrown toenails or explosive diarrhea. Logan ascertains that, if the stories of the Small Folk are true, then they will need more than claws and webs to save the world.
Suddenly Logan cares about this world, Spider-Man questions doubtfully. That must be why he holes himself up fighting power drills and toasters. He points out that the Small Folk have been outside for months and asks if Logan has ever gone to talk to them. Logan simply denies that he is the Messiah they think. Spider-Man counters him saying that Logan was right to live with all the Small Folk back in prehistoric times. He taught them to fight and stand up for themselves, and that changed the future. Instead of dying out with the dinosaurs, the Small Folk, who had been living in the shadows, took over after the fall of human society, making sure that this world was not completely dead. If the Small Folk hadn't passed down stories of Wolverine for the last 65 million years and recognized him when they first popped into this time period, then Devil Dinosaur would have ripped them to shreds. “Ripped you to shreds maybe,” Logan mutters.
Spider-Man ends his speech by claiming that he doesn't know why they are here, and while time travel makes him nauseous, he knows in his heart that they are there for a reason. After Logan chuckles at this, Spider-Man comments that the first time Logan laughs at something he said was when he wasn't trying to be funny. Command code Beta Charlie Seven, replies Logan. Parker's cue to leave, he informs Peter.
As the robots prepare to attack the two heroes, Spider-Man claims he'll stick around, since talking to Wolverine always makes him want to hit things. As Spider-Man high jump kicks the head off a robot, he asks if Wolverine hates him or just himself. Is Peter the brother he never had or something? As Wolverine slices down a robot, he answers that he had a brother, and he tried to kill Logan. Peter isn't surprised as he thinks about killing Logan every day, despite him being the only other human left. Logan doubts that Peter could kill a fly. With the proportionate strength of a spider, of course he could kill a fly retorts Peter. Wolverine remarks that he can never tell when he is joking. “I think you're a swell guy to be stuck in a post-apocalyptic wasteland with,” which Peter immediately explains is a joke.
As much as Peter would love to stay and keep killing robots with Logan, he figures that, with the end of the world coming, he should do something that isn't a complete waste of time. Among the wreckage, Logan solemnly admits to Peter that back in the jungle he found someone watching him. Despite Logan going out hunting every night and finding nothing, he knows that they're being watched. Spider-Man claims this is even more reason for them to go out and fight. Wolverine tells him that he should know that, when it comes time to fight, he will be there. The people outside Logan's door don't need him riding in like cavalry, but they need hope, which he can give them just by opening the door. Logan can't bring himself to be their messiah. Disgusted, Spider-Man leaves, claiming he understands that killing is easier than inspiring and that should make a great legacy. Ashamed, Logan offers Peter a drink, but he is already gone.
As Spider-Man swings back toward his house, he swears that he could strangle Logan, even though he has never been the type to strangle. He thinks maybe they are being watched but has long since exhausted himself trying to figure this all out. He wishes he could have a good old fashioned victory, something he hasn't had in a long time. He can accomplish it by saving this world from annihilation, then he can concentrate on other problems. He looks over at some carvings of a woman on his desk and wonders why he still sees her in his dreams every night. He has no idea who she is, but he can sense that she is lost out there just like him. He must find her if it is the last thing he ever does, though preferably it won't be.
A giant laser blasts through Spider-Man's locked weapon storage room, narrowly missing a ducked Spider-Man. A heavily muscled Orb, dressed and armed like a commando, steps out and recognizes Spider-Man. Orb immediately demands for Spider-Man to tell him where he is hiding “them.” A confused Spider-Man suddenly finds himself dodging blaster fire as Orb screams “Tell me where they are!” Spider-Man webs up Orb's gun hand and asks who Orb is talking about and what is going on. He complements Orb, saying that he seems much less lame than last time they met, and he should know considering his butt.
Orb tells Spider-Man that he can't even imagine the places that he has been and the things he has experienced. He has to keep going, despite almost being out of fuel, or the Minutemen will catch him. Orb knows that Spider-Man is also traveling and wants to know where his fuel, the diamonds, are located. Spider-Man is confused again and refers to the diamonds at the bank, asking if he should have diamonds, because he certainly doesn't. Orb pulls out a knife and descends on Spider-Man, calling him a liar and claiming this is all his fault. Orb hopes that he will get to watch when Spider-Man realizes… A portal opens behind Orb and two metal arms grab him from behind. As they pull Orb through the portal, he howls in rage and fear that they found him, yelling that it's the Czar they really want. Spider-Man reaches to pull him back, but it is too late.
Spider-Man reviews these new revelations of on-the-run villains, mysterious diamonds and cryptic references. He is used to this kind of thing and he just needs to figure out what to do now. A speaker phone declares an emergency at “site 17” and pleads for someone to get out there, as they have found something.
At the site, Spider-Man follows a digger underground to an uncovered bunker decorated with the X-Men symbol. The foreman claims that the digger who found the object said it burst into flames and the fire was cold as ice. When he asks Spider-Man if he knows what it could be, everyone stares down at a briefcase with a brightly glowing phoenix symbol.
Having taken the case back to his weapons lab, Spider-Man studies this object with its bone chilling symbol for several hours. He comes to the conclusion that this object can save them, but someone will have to die use it. As he swings back to explain everything to the elders, his spider-sense goes ballistic. “He” is here and Peter never would have believed it if he hadn't seen it with his own eyes. Surrounded by the Small Folk, Spider-Man stares up in awe at the sky at what the Small Folk call the god moon. Spider-Man knew him as the despotic would-be world conqueror, Victor von Doom, but now he is something greater.
Doom the Living Planet fills the entire sky and its surface appears as a giant mechanical Dr. Doom mask, the giant eyes and mouth of which burn like fire. The legends say an aging Doom managed to transplant his consciousness into the only thing large enough to contain his ego, a whole planet. This process wiped out nearly all life on Earth. Doom bellows out in a massive voice to “Release the Heralds of Doom!!!” Giant robot bugs ejected from his surface, crash into the city as Doom cries out “Make Ready for Annihilation!!!”
Spider-Man thinks about how he thought he was bad when he was just a creepy nutcase in a metal mask. Farther back, Devil Dinosaur roars loudly as the Small Folk run towards his perceived safety. Spider-Man stops him from attacking the bugs and tells the rider that he needs to lead the Small Folk to safety. When the rider protests, claiming he needs to show them that Devil Dinosaur rules the wasteland, Spider-Man replies that he can do it tomorrow, assuming there is a tomorrow. As Devil rides off to help the people, Spider-Man slowly walks forward, thinking about how he now has to fight a talking planet. He asks if anyone else would like to be him right now, because he definitely doesn't.
While the giant bugs attack and burn everything, Peter stands over the glowing briefcase. He thinks about how the Phoenix Force is a crazy powerful cosmic firebird that seems to be attracted to earthbound red heads, to which he can relate. The Force likes to possess them, make them go crazy and blow up planets. He pulls out a clear bullet, encasing a bright flame inside, the Phoenix Force cast into a bullet. He also pulls out the gun that fires it, wondering who made it and why. This is what they need to save them and he would be more excited except that it will also splatter his atoms across the cosmos. According to his figures, whoever pulls the trigger will be ripped apart at a subatomic level.
Peter concludes that no one lives forever anyway, but it would have been nice to try. As he prepares the gun, he can barely concentrate with his raging spider-sense. He hopes he doesn't miss, since he can't remember the last gun he fired a real gun… Whack! Spider-Man falls unconscious to the floor and Wolverine picks up the gun, telling Parker that if one of them has to shoot something, even if it is as big as a planet, it ought to be him. He tells Peter to sit this one out and cradles the gun fondly, saying that Jeannie and him got this.
As Wolverine walks calmly towards his destiny, two figures watch from a distance, conversing. About time says the first, he can't stand much more of this. The other one tells him to be cool boss. The first tells him to shove it, as these two dudes are making him sick. They were funny at first, in a pathetic crippled kids or old people way, but all they do is bicker. It is like living with his parents before he killed them. The second smaller figure reminds him that the Big Man's paying good money for all this and the Czar always delivers.
The bigger figure agrees that he does pay good money but the little simple pleasures are what make life worth living. Like a good steak or a good woman the small guy asks? Two hands holding a diamond encrusted bat belong to the figure who replies, no like snapping a guy's neck when he gets on your nerves he explains. Through teeth coated in diamonds, he continues. It's like his grandmother always said, “Sometimes you gotta just cut the $%*#... and get down to the part where somebody's dyin.”