Time Crisis is a story line created to celebrate the 75th anniversary of the character. It features a temporal rift that causes Peter to encounter his teenage self, about two weeks after his uncle's death. The story featured two art styles: the modern, realistic art style that turns young Peter Parker into a more modern form; and the classic art style with bright colour backgrounds that cause modern characters to resemble themselves at that point in time.
In the past (resembling the original art style of the 1960's spiderman comics) Peter Parker was walking through his school. He is attacked by Eugene Thompson while he was distracted. While Peter pretended to be weak, Flash began saying how he is going to make it big in the future while Peter won't. Silently, Peter replied that with his luck, the future is going to have really unexpected surprises.
In the present, Peter is web swinging, thinking about that day in his youth, noting he had been right as he remembered all the things that happened, ranging from all his enemies, Gwen Stacy's death, his clones, joining the avengers, coming back from the dead, the spider-verse event, and becoming a temporary member of the guardians of the galaxy. Peter entered his shared apartment with Anna Maria, who he is surprised to find with Mary Jane, Cindy Moon and Carlie Cooper.
Carlie reveals that she has returned to get a few things and check up on Peter. Mary Jane, having left for Venice long ago, has returned for an acting opportunity. After a conversation where the four girls talk about their relationships, specifically Peter, Peter begins feeling unwell, before collapsing.
Back in the past, Peter is moaning about Flash when his spider sense goes off. A split second later, the wall to the school exploded, to reveal the goblin knight (reimagined to look as if he belonged in the classic time) who screams for spider man. Peter races off to get into costume, before reappearing to fight. However, he is instantly struck by the villain.
At the exact same time past Peter was hit, present Peter screamed in pain at avengers tower, where he was taken by his three ex girlfriends to seek aid. While captain America interviews them, the rest of the avengers investigate Peter, who continues to scream each time past Peter is hit by goblin night.
As goblin night prepares to finish the weakened teenager off, Peter is saved by spider man 2099, who drags Peter away. In the present, Peter awakens, screaming something had gone wrong. As young Peter and spider man 2099 swing away from goblin night, Peter tries to explain the dream he had of the fight to the skeptical avengers. In the past, Peter and spider man 2099 are attacked as a portal opens, which Peter is pushed into by spider man 2099.
Back in the future, Peter again screams in pain as the Tony Stark arrives, with Peter fading slightly. After investigating, Stark comes to the shocking conclusion that Peter's personal timeline is being altered, with his dream being his new memories being created.
At that moment, avengers tower began to alter slightly and, after looking through the databases, they found that Peter joining the avengers has been erased from history, making them realise that his timeline wasn't just being altered: it was being threatened by an outside force that might be specifically targeting spider man.
Switching back to past Peter's point of view, he awakens to find himself at night. Confused, Peter web swinged away, before encountering agent venom, coming back to Earth to get a few things. A fight quickly escalates between the two when venom's host, Flash Thompson, realizes Peter doesn't know who he is. In a shocking fight, Peter is nocked unconscious and has his mask removed, shocking Flash.
Meanwhile, present Peter gets the aid of Kain and Miguel O'Hara (having previously returned to Peter's time to battle his evil future self and becoming trapped again), needing help understanding what was happening. While Miguel states it should be impossible, he is proven wrong when agent venom arrives with the young Peter, shocking everyone in the room and revealing present Peter's secret identity to Flash. Before they could explain, young Peter wakes up and escapes, forcing present Peter to chase after him.
Swinging through the city, the two Peters finally clash, with past Peter holding his own with his stronger powers due to his youth while present Peter challenges his past self with his greater experience. While this is happening, the avengers attempt to discover the source of the disturbance, with Flash feinting and experience his memories altering. Stark also finds another large temporal anomaly manifesting.
Kain and Miguel arrive to help present Peter, with past Peter becoming distracted with Miguel's arrival. This lets his older self overpower him and attempt to talk to him. Calling himself Pete, due to it sounding older, he tried to reason with the confused Peter, before they were attacked by Eddie Brock, as venom.
As the avengers go off to find Peter, Flash finds his venom suit evaporating slightly, much to their confusion. Meanwhile, the four spider themed heroes struggle to fight Eddie, with Pete unable to figure out how Eddie is venom again. At that moment Flash arrives, making Eddie confused long enough for him to be captured.
Back at avengers tower, Peter communicates with Pete and everyone, slowly accepting he was in the future. However, Miguel says they have to fix this, as the events happening shouldn't be and if it continues, Pete may be erased. Interrogating Eddie, they learn he was offered by doctor octopus a chance to kill spider man, which he accepts. They also learn that octopus recruited him into a new team composed of villains from Spiderman's past, with the chilling desire to destroy spider man during the first few weeks of his arrival. However, he refused to tell them which villains were part of the team.
While the Pete works with the avengers, Peter ends up talking to Kain, Miguel, Flash and his future ex girlfriends. He is shocked that he inspires other heroes, but he goes into instant disbelief when he learns he is friends with Flash. When he learns that he will one day date girls "who are out of everyone's league", Peter becomes interested in what else the future had to offer. Taking off, Pete curses his younger self's solo and independent attitude before following. Just as Pete leaves, iron man shows up with the results
While Pete is talking to Peter, iron man informs everyone that slowly, events in the past related to spider man in any way is slowly being erased, most likely due to the teenage Peter being in the present. He predicts that they have a twelve hour window of opportunity to return Peter to the past before Pete is fully erased and everyone forgets him, and the world changes.
At that moment, the two Peters are attacked by two versions of Mac Gargan: one as the scorpion and one as venom. Teaming up, Peter is amazed by Peter's fighting skills against venom, to the point he is distracted long enough for scorpion to escape.
Returning to avengers tower, Peter scowls himself for failing and rudely ignores his future self's attempt to help him, getting angrier when spider woman pointed out that it was pointless to be jealous of Pete as they were the same person. Furious, Peter left and Miguel followed him. While this happened, Pete began to fade away.
Peter finds himself at Parker Industries, further surprising himself of the future. When Miguel arrives, Peter asks him what was the bad side of his future. Grudgingly, Miguel admits that the cost of this future was alot of pain and misery along with hundreds of enemies. Upset, Peter web swings to his old house, finding it deserted. Peter begins feeling emotional stress to his situation, afraid of what happened to aunt May and everyone else. After a heart to heart talk with Pete,who had followed him, Peter sadly goes with him as Pete truthfully begins telling him the good parts of his life and the bad.
At Parker Industries, Pete is picking up a few things following a battle with the original mysterio and mysterion when aunt May, Liz Allen, Betty Brant, Robbie Robertson, J Jonah Jameson Jr and J Jonah Jameson Sr walk in and see the two Peters. Quickly, Pete comes up with the story that a machine he built somehow brought his younger self to the present.
He asks what they are doing here and explain they are here for his birthday. Peter is shocked that Liz Allen is his friend and nearly has a panic attack when he learns she is his ex-girlfriend. While Peter wants to stay, much to Pete's annoyance, JJJ quickly makes him run away by telling him that his aunt married the formers father, making them related. Horrified, Peter begins begging Pete to take him back. At that moment, Pete begins fading, forcing him to reveal that Peter was never meant to be here, meaning history is changing and if it continues, Pete might cease to exist.
Suddenly, a blackout appears, before two bright lights appear, belonging to two versions of electro: one before losing his powers and one wearing his classic costume. Getting into costume, they head off to fight them. However, upon arriving it is revealed that it was a trap, as doctor octopus arrives with his team the spider slayers. The team is made up of every spider man villain in every incarnation since his arrival. In the resulting fight, where the crowd quickly realise that time travel is involved, the Peter of the present is killed saving lives before being unmasked, shocking everyone. Peter is terrified as he realises that he has just been killed and begins losing all hope. However, before he is killed he is saved by the x men and daredevil, who help him escape with the aid of many other heroes.
At Avengers tower, all the heroes who are allies to spider man are preparing to fight. However, Peter has lost hope despite their obvious chance of winning. Despite everyone trying to help, telling him of who he will become and telling him they might be able to stop his death, Pete is angry and distraught over his future death.
Sadly following, Peter begins talking with many great heroes, who start telling him of many shared adventures and how their friendships were formed. When they arrive, the united team of heroes struggle to fight the vast amount of villains, which is larger than any anticipated. However, seeing that they were willing to sacrifice themselves for him, Peter snaps out of his depression and begins fighting. He quickly adapts to fighting his foes, making jokes and quips as everyone stares in awe. However, the villains manage to escape.
Talking with the heroes, they all agree to split up to try and stop the villains and help the city. Spiderman 2099 takes off to try and find the anomaly with iron man, silk and spider woman; scarlet spider attempts to hunt down the villains with captain America, punisher, agent venom and Luke Cage; and daredevil, Thor, the thing and the prowler protect the younger Peter. While all this happens, the x-men and every other hero will work on restoring order to the city of New York.