The story opens with Spider-Boy fighting the Scavulture [Vulture/Scavenger] is fighting Spider-Boy in the man-made caverns of New York City. The Scavulture uses his evil eye to cut Spider-Boy's webline, causing the arachnid youth to fall into a dumpster in Suicide Street [Yancy Street/Suicide Slum]. After a quick recovery, Spider-Boy is unable to find his web-shooter (an actual gun in this universe). However, it's fallen into the hands of the Yancy Legion [Yancy Street Gang/Newsboy Legion], a group of juvenile delinquents. As Spider-Boy chases after their newest member to retrieve the web-shooter, the Scavulture plows into Spider-Boy from behind, causing him to fall down and bemoan the lack of some sort of radar sense to know when danger is coming. The Scavulture is about to finish Spider-Boy off when a cube comes and freezes time around Spider-Boy.
Elsewhere, Spider-Boy's manager, Rex Leech, is putting together the details of Spider-Boy's wedding to the Insect Queen while Otto Octavius and Betty Brant stand around. Rex is interrupted when a silver figure on skis flies in. They seem to know who he is, but the figure deems that they have no role in what is about to happen, and so he knocks them out proclaiming that he, the Silver Racer [Silver Surfer/Black Racer] must watch as a hero falls. This event will not happen in this issue, but in "Challengers of the Fantastic #1".
Elsewhen, Spider-Boy is out of his cube and is being greeted by more youthful super-heroes in the year 2099. He finds out the cube he was in was the Time Square [Time Cube/Time Sphere]. Spider-Boy asks who leads the youths, and they say they're about to elect a new leader from their roster. The roster of the Legion of Galactic Guardians 2099 [Guardians of the Galaxy/Legion of Super- Heroes]. Psi Girl [Psylocke/Saturn Girl] informs Spider-Boy that the Legion was created because of his deeds. He says that he likes this future, but Martinex 5 [Martinex/Braniac 5] informs Spider-Boy that he can't stat for longer than nine minutes, as if he does, the universe may suffer complete chronal collapse.
Spider-Boy is understandably worried, and posits that even knowing about the Legion may risk some sort of snafu in time. For example, he may do something that causes the Legion to never exist at all. Universe Boy [Captain Universe/Ultra Boy] tells him that the Arach-Kid doesn't have much future left. Martinex 5 shushes him, and Spider-Boy figures that he's going to be returned to where Scavulture was about to kill him and die. As they're about to send him back, though, the Frightful Five [Frightful Four/Fatal Five] smash into the Legion clubhouse and destroy the Time Square generator. Martinex 5 bemoans the situation, a cloaked figure sneaks up behind Spider-Boy (we get a brief cameo of Spider-Man's right arm here). Another figure in a Time Square tells Spider-Boy to come with him if he wants to live, and after evaluating the situation, the arachnid youth decides not much worse can happen, and leaps into the Time Square, ending up five years in the future.
In that era, Spider-Boy meets what's left of the Legion after the collapse, and they tell him he must go back to when it all began. Looking at the desolate future, Spider-Boy agrees, and leaps back into the Time Square, ending up once again at the clubhouse of the Legion of Galactic Guardians 2099. This time, however, things are a bit different. For one, the roster of the Legion is a bit different and smaller, and Spider-Boy was only brought there on advice on how to operate a Phantom-Negative Zone Projector. Spider- Boy gets it working by having 'Lectron [Electro/Live Wire] pour electricity into it, and then Spider-Boy hops into the Time Square to go back to his own time, and supposedly, death.
However, Spider-Boy evades Scavulture's blast, but the villain is still keen on turning Spider-Boy into a corpse. The new member of the Yancy Legion sees that the archnid youth needs help, and uses the web-shooter he stole from Spider-Boy to help even the odds at the cost, seemingly, of his life. At this point, however, the Yancy Legion reveals itself to be several members of the Legion of Galactic Guardians 2099. They make short work of the Scavulture, and then the five Legion members and Spider-Boy escort the stricken youth to the empty facilities of Project: Cadmus and send the youth to the Phantom-Negative Zone where he'll be kept in stasis until help can be found. As Spider-Boy begins to search for answers, time once again freezes, and the cloaked figure from his first meeting with the Legion arrives again, this time revealing himself to be Kang, the Time Conqueror [Kang the Conqueror/Time Trapper].
Kang transports himself and Spider-Boy to Limbo. Kang wants to use him to conquer the omni-verse by splitting him apart and absorbing the life energies of his amalgamated forms. This allows for another cameo of Spider-Man, this time his entire right half and a line of dialogue (Spider-Man: Hey!). The plan is halted when another Time Square arrives with a youth with powers similar to Spider-Boy. He forces Spider-Man and Superboy to re-merge, and then joins forces with Spider-Boy to stop Kang's plot. After webbing him up a lot, they unmask Kang, revealing Chronos-Tut, the Time Pharaoh [Rama Tut/Chronos] who looks and talks like Richard Nixon. However, unmasking Kang or Nixon or Tut or whatever negated his abilities to control the Omniverse, and there's a big explosion.
Spider-Boy and his ally return back to the point before Spider-Boy was abducted. The ally tells Spider-Boy that his name is Spider-Boy 2099 (Mig-El Rand) [Spider-Man 2099/M'Onel] and that Spider-Boy created a cure years later to save Spider-Boy 2099's life, and that the original Spider-Boy has quite a future ahead of him. The Legion members leave with Spider-Boy 2099, and Spider- Boy is left really confused about the time-spanning adventure he just had.