Arc 3Hydra’s Hidden Research

Peter helped stop Loki’s invasion, then uncovered his parents’ connection to a Hydra serum project and traced it to Herbert Wyndham. Wyndham kidnapped Aunt May and Uncle Ben to obtain the research, leaving Peter and his allies preparing to pursue him at Treadstone.

  • Peter confronted Charles Xavier over reading Felicia’s mind, and Jean accepted Xavier’s offer to attend his school before sharing a farewell night with Peter and Felicia.
  • Peter joined the Avengers against Loki’s Chitauri invasion, helped evacuate civilians, and revived Tony after the portal closed, and afterward, he celebrated his birthday and began investigating his parents’ past.
  • Peter found recordings showing Richard and Mary had worked on a Super Soldier Serum project and discovered that the evidence pointed to Herbert Wyndham.
  • Peter searched Wyndham’s files in Italy, encountered Jessica Drew, and later told Felicia the truth about his investigation and Jessica’s kiss.
  • Peter gave Fury his parents’ research hard drive, but Wyndham learned Peter’s identity and kidnapped Aunt May and Uncle Ben to demand the research.
  • Peter and Felicia stole the hard drive back from the Helicarrier and exchanged it for his relatives, only to discover Wyndham had used decoys and was threatening them again.
  • Peter, Johnny, and Felicia fought Wyndham, Sandman, and Jessica at the construction site, while Peter secretly tracked Wyndham toward Treadstone.
  • Fury assembled the X-Men and Jessica to pursue Wyndham, and Natasha introduced her special asset, whom Felicia recognized as her father.
Chapters 51–75 Vol. 1 Read

Ch. 51Nonmagnetic Iron Fist

Peter defeated Magneto, then confronted Charles for entering Felicia’s mind and threatened him against ever manipulating the minds of people he cared about. After warning Magneto about abusing power, Peter reunited with Felicia and revealed his face to the others.

  • Peter beat Magneto until Wolverine tried to intervene, and he threatened Wolverine with a mechanical arm.
  • Peter learned that Charles had entered Felicia’s mind and accused him of violating her privacy.
  • Peter fought past Wolverine, confronted Charles, and demanded that he never touch the minds of Peter’s loved ones again.
  • Peter warned Magneto that humans were not weak and told him that their next meeting would go differently if he continued abusing his powers.
  • Felicia hugged Peter, and he reassured her before opening his helmet and greeting Mary Jane, Liz, and Jean.

Ch. 52Separation

After Magneto attacked Peter and his friends, Peter called S.H.I.E.L.D. to arrange a secure cell while challenging Charles Xavier over invading minds and exposing his identity. Jean accepted Charles’s offer to attend his school and learn to control her powers, leaving her friends worried as Peter questioned whether the choice was truly her own.

  • Peter called David and told him to prepare a treated titanium cell for the unconscious Magneto, while Charles said he had kept Magneto in an induced coma.
  • Peter confronted Charles for reading Felicia’s mind and revealing Peter’s secret identity, then learned that Charles had come to recruit Jean as a student at his school.
  • Ororo and Logan introduced themselves to the girls, and Liz and Mary Jane discovered that Peter was Spider-Man.
  • Peter explained that he had kept his identity from Mary Jane because she had been dating Harry, upsetting her.
  • Jean accepted Charles’s offer after speaking with him telepathically, despite Liz and Mary Jane urging her to stay.
  • Peter warned Charles that Jean might not know whether the decision was truly hers, while Felicia encouraged Jean to learn to control her abilities.

Ch. 53Three Together

Jean prepared to leave New York for Xavier’s school after S.H.I.E.L.D. took Magneto away, spending her final day with Peter, Felicia, Liz, and Mary Jane. At the end of the night, Jean confessed her feelings for both Peter and Felicia, and the three chose to stay together.

  • Jean said goodbye to Peter and her friends before S.H.I.E.L.D. took Magneto away, and Charles promised to speak with her parents.
  • Charles persuaded Jean’s parents to let her attend the school, and Peter helped Jean and the girls pack her belongings.
  • Peter revealed to Liz, Mary Jane, and Jean that he was Spider-Man and explained how he gained his abilities and met other heroes.
  • Liz organized a farewell party for Jean at Mary Jane’s house, where the friends played Monopoly and drank together.
  • Jean kissed Peter and Felicia, confessed that she liked them both, and Felicia admitted she loved Peter.
  • Peter, Felicia, and Jean went into a guest room together, and none of them changed their minds.

Ch. 54Clouds and Rain

After an intimate night with Parker and Felicia, Jean reassured Parker about Felicia’s feelings and prepared to leave with Xavier. Jean departed for Xavier’s school, while Parker and Mary Jane walked home and he pushed aside an ominous thought about Jean’s future.

  • Mary Jane opened the bedroom door, saw Parker, Felicia, and Jean together, and hurriedly closed it after realizing she wanted to join them.
  • The next morning, Jean told Parker that Felicia loved him and would not leave him, then Mary Jane took Jean upstairs to ask her to promise something.
  • Parker, Mary Jane, Felicia, Jean, and Liz ate breakfast before Jean gathered her luggage and said goodbye to everyone.
  • Xavier arrived with Logan and Ororo, and Jean left with them after telling Parker that Mary Jane had a crush on him.
  • Parker and Mary Jane walked home, and Parker mentioned the possibility of Jean becoming a world-destroying cosmic monster before dismissing it as an inside joke.

Ch. 55Avengers assemble 1

Peter prepared for the Avengers Initiative after Fury recruited him to help recover the stolen Tesseract. He joined the team aboard the Helicarrier, and the chapter ended as he and Captain America jumped toward Loki in Germany.

  • Peter rebuilt his equipment and secretly began investigating whether he could gain mutant abilities from Magneto’s blood.
  • Fury briefed Peter on the Avengers Initiative and revealed that the Tesseract had been stolen.
  • Peter boarded a S.H.I.E.L.D. jet with David, concealed his identity from most of the Avengers, and arrived at the Helicarrier.
  • Peter met Bruce Banner, Natasha, and Captain America aboard the Helicarrier as S.H.I.E.L.D. searched for Loki and the Tesseract.
  • S.H.I.E.L.D. located Loki in Germany, and Peter jumped from the jet with Captain America while Natasha covered them.

Ch. 56Thor

Peter and Captain America helped capture Loki, but Thor attacked their jet and freed him. Peter was badly injured and lost consciousness as Iron Man and Captain America pursued Thor.

  • Steve reflected Loki's beam with his shield, and Peter joined him in fighting Loki.
  • Peter and Steve weakened Loki until Iron Man arrived and forced him to surrender.
  • On the jet, Tony discovered that Peter had built improved armor using Stark technology and parts from Justin Hammer's drones.
  • Thor crashed onto the jet, and Peter blasted him out before Thor struck Peter and freed Loki.
  • Iron Man and Captain America went after Thor while Natasha tried to help Peter, who collapsed unconscious.

Ch. 57Emergency Notice

Peter woke in the hospital after the Avengers had fractured and helped Tony and Steve move past their grief over Coulson’s death. They identified Stark Tower as Loki’s target, headed for Manhattan, and Peter warned the public to evacuate, though people dismissed his post as a stunt.

  • Peter learned from Natasha that Loki had escaped, S.H.I.E.L.D. had suffered heavy losses, and the Avengers had fallen apart.
  • Peter confronted Tony and Steve in the Hulk’s empty cell, revealed his young face, and urged them to stop blaming themselves and fight Loki for Coulson.
  • Peter explained that Loki had let himself be captured to divide the Avengers, and the three realized Stark Tower was the stage for Loki’s planned spectacle.
  • Tony flew off to suit up while Peter and Steve went to find Natasha and Hawkeye.
  • Natasha piloted the Quinjet toward Manhattan with Clint, Steve, and Peter aboard, and Peter posted an emergency evacuation warning that people dismissed as a stunt.

Ch. 58Battle of New York

Peter warned New Yorkers to evacuate and called for help as Loki’s portal opened above Manhattan. The battle began with the Chitauri invasion, and Peter and the others faced a Leviathan as alien troops swarmed into nearby buildings.

  • Peter had Steve record an urgent evacuation message, which spread online and prompted police to clear blocks around Stark Tower.
  • Peter called Johnny and Susan in Germany for help, then warned Felicia to keep away from Manhattan and learned Liz was there for work.
  • A blue portal opened above the city, and thousands of Chitauri craft poured through while Tony led them toward the others.
  • Loki shot down Natasha’s jet as it approached Stark Tower, and Peter helped the survivors escape the crash.
  • Peter prepared to carry the group back up toward the tower when a Leviathan emerged from the portal and Chitauri soldiers invaded nearby buildings.

Ch. 59Avengers, assemble

Peter rescued civilians and fought the Chitauri alongside the Avengers as the invasion intensified. With Bruce arriving and Hulk destroying a Leviathan, the heroes regrouped under Captain America’s lead and prepared to fight together.

  • Peter entered a building, killed the Chitauri attacking civilians, and directed the survivors to hide.
  • Peter battled Chitauri flying craft and ground forces, then joined Natasha and Clint in the street.
  • Captain America and Thor arrived to help, and Thor explained that he could not break through the energy around the Tesseract.
  • Bruce reached the team on a scooter, and Tony lured a Leviathan toward him.
  • Bruce transformed into Hulk and punched the Leviathan into the air, allowing Tony to destroy it with a missile.
  • Captain America, Thor, Tony, Hulk, and Peter stood together amid the rubble as the surrounding Chitauri closed in.

Ch. 60The last minute

Peter and the Avengers fought to contain the Chitauri invasion while civilians evacuated, and Tony carried a nuclear warhead through the portal. Tony returned just before the portal closed, and Peter revived him as the battle ended.

  • Captain America assigned the Avengers to hold the Chitauri within the combat zone, while Peter trapped their flying craft in webs.
  • Peter fought beside Felicia, then convinced her to lead civilians to safety.
  • Peter helped the police and military repel the Chitauri, fought alongside Captain America, and was wounded by a plasma blast.
  • Natasha said she could close the portal, but Tony revealed that a nuclear warhead was headed for the city and flew it through the portal.
  • Peter urged Captain America to wait before closing the portal, and Tony fell out just before it sealed; Hulk caught him, and Peter revived him with bioelectricity.

Ch. 61Birthday

After the Avengers defeated Loki, Peter celebrated with the team and realized it was his birthday. He left with Felicia, reassured her that her actions made her a hero, and ended the day with her on a train heading toward Queens.

  • Tony invited Peter and the others to get shawarma after Loki was captured and handed over to S.H.I.E.L.D.
  • The group discussed becoming a public team, and Peter posted a photo declaring that the Avengers were not breaking up.
  • Felicia arrived, and Peter introduced her as his girlfriend; Natasha gave him a S.H.I.E.L.D. contact as a birthday gift, prompting Peter to realize he had forgotten his birthday.
  • Thor promised to bring Peter a weapon from Asgard, and Peter left with Felicia after agreeing to keep in touch with the others.
  • On a train bound for Queens, Peter learned Liz was safe and told Felicia that saving her friend had made her a hero.

Ch. 62Father

Peter celebrated his birthday with Aunt May, Uncle Ben, and his friends, then received his late father’s old DeLorean. The next day, after meeting the Avengers and collecting alien technology from the ruins, Peter narrowly dodged a barrage of bullets.

  • Peter celebrated his birthday with Aunt May, Uncle Ben, Felicia, Mary Jane, and Liz, who thanked him for saving her.
  • Uncle Ben gave Peter his father Richard’s battered DeLorean, and Peter gratefully accepted it.
  • Felicia joined Peter in bed that night after explaining that Liz and Mary Jane had mistaken a photo of Spider-Man kissing Black Cat for Peter cheating on her.
  • Peter met Natasha and the Avengers in Central Park; Natasha recognized Felicia and arranged to resume Peter’s intensive training.
  • Peter gathered Chitauri weapons and armor from the ruined parts of New York, then jumped clear when his Spider-Sense warned him of gunfire from scavengers.

Ch. 63Gradually recovering

After the Battle of New York, Peter settled into life as a widely admired hero while investigating alien technology and continuing Natasha’s training. As order returned to the city, he began planning a DeLorean overhaul and called Johnny for help.

  • Peter captured a group of armed men, but an unseen ally killed the captives before they could reveal who they worked for; Peter found a skull tattoo on the surviving shooter and contacted Fury.
  • Weeks after the Battle of New York, Peter enjoyed growing public support, helped the Baxter Building team, and secretly paid off Uncle Ben and Aunt May’s overdue bills.
  • Peter used alien technology to make his mechanical spider arms safer, analyzed the aliens’ armor alloy, and helped Reed reverse-engineer their energy batteries.
  • Natasha continued Peter’s combat training and began teaching him surveillance and interrogation skills.
  • As New York recovered and Peter spent less time fighting crime, he called Johnny to ask for help modifying his DeLorean.

Ch. 64Modifications

Peter and Johnny transformed Peter’s DeLorean into a flying car, then Peter took it home and drove Mary, Liz, and Felicia to Xavier Mansion to visit Jean. The group reunited with Jean at the mansion, where they had just arrived.

  • Peter, Johnny, and Ben replaced the DeLorean’s engine and upgraded its interior, suspension, and safety systems, while Peter and Johnny secretly installed repulsor cannons.
  • Peter and Johnny activated the car’s flight mode and raced above the East River, then Sue reprimanded them and took the motor blueprints to reassure investors.
  • Peter brought the modified car home, showed it to Uncle Ben, and later took Felicia and Liz’s father for rides before agreeing to visit Jean with the girls.
  • Peter, Mary, Liz, and Felicia drove to Xavier Mansion, where Logan let them through the gates and Jean ran out to greet them.

Ch. 65Scott

Peter visited Jean at Xavier’s mansion with Felicia, Liz, and Mary Jane, met Scott, and confronted Xavier about his use of psychic powers. He invited Xavier and his team to join the Avengers, and Xavier agreed to help when the next threat came.

  • Peter reunited with Jean and gave her and the other girls upgraded earrings and headbands that blocked psychic detection.
  • Jean introduced Peter and his friends to Scott Summers, who led them on a tour of the mansion and grounds.
  • Peter warned Xavier not to read their minds and challenged him over his past use of psychic powers, while Xavier apologized but stood by his actions.
  • Xavier offered Peter a chance to teach at the school, and Peter invited Xavier and Ororo to join the Avengers.
  • Xavier agreed that his team would help the Avengers, while Ororo warned Xavier that Peter’s anger could become his downfall.

Ch. 66The storage room

Peter visited Xavier's school, beat Scott at basketball, and helped Logan recognize himself in a World War II photograph, giving him a lead on his lost past. On the drive home, Peter resolved to investigate the storage room that had belonged to Richard Parker, sensing the search could lead to danger.

  • Peter challenged Scott to basketball and won, earning the chance to ask about Scott's power.
  • Peter examined Scott's eyes and suggested his energy might come from another dimension.
  • Jean secretly invited Peter to spend time alone with her and Felicia next time they visited.
  • Peter showed Logan a photograph of him with Captain America, helping Logan realize his identity and prompting him to ask to speak with Rogers.
  • Peter and the girls headed home, and Peter decided to explore his father's storage room downtown.

Ch. 67Hydra's Weapon (1)

Peter confronted teenagers who were imitating him as the Web Warriors, then spoke with Tony about his PTSD and Peter’s father. The chapter left Peter asking Tony to investigate his father through S.H.I.E.L.D.’s database, and Tony agreed.

  • Peter warned Chad and the other Web Warriors to stop fighting crime in his name and wearing his symbol.
  • Peter met Tony Stark on a rooftop and asked whether he was coping with his PTSD; Tony said he was getting better by focusing on inventions.
  • Peter told Tony that his father had experimented on him as a baby and might have caused his powers.
  • Tony urged Peter to find out what his father had done, and Peter asked him to investigate using S.H.I.E.L.D.’s resources.
  • Tony agreed to hack into S.H.I.E.L.D.’s database without alerting Fury or anyone else.

Ch. 68Hydra's weapon (2)

Peter searched his parents’ belongings and unlocked Richard’s encrypted files, discovering that Richard and Mary had worked on a super-soldier formula at a secret institution and fled after realizing their colleagues were disappearing. The evidence left Peter with one lead: Herbert Wyndham.

  • Peter and Uncle Ben retrieved Richard and Mary’s belongings from storage unit 342, and Peter took the old hard drives, books, and papers home.
  • Peter unlocked Richard’s encrypted file using the nickname “STR-SPIDER” and watched recordings of his father’s research.
  • Richard’s videos revealed that he and Mary had joined a secret project to recreate Dr. Abraham Erskine’s Super Soldier Serum, using a mysterious book they suspected Erskine had written.
  • Richard and Mary said their colleagues were disappearing and that they planned to flee after contacting the government for help.
  • In the last recording, Richard and Mary said they had perfected the formula, feared it would fall into the wrong hands, and had saved evidence identifying the person behind the project.
  • Peter examined the remaining files and found that the evidence pointed to Herbert Wyndham.

Ch. 69Hydra's weapon (3)

Peter traveled secretly to Italy with Tony Stark to investigate Herbert Wyndham, the researcher he believed was connected to his parents’ deaths. After breaking into Wyndham’s home to copy his files, Peter was discovered by the old man.

  • Peter found that Herbert Wyndham was a geneticist living in Italy and arranged with Tony to fly there without leaving an immigration record.
  • Peter told Tony that his parents had tried to replicate the Super Soldier Serum and that Wyndham might have been tracking them.
  • Peter said goodbye to Uncle Ben and Felicia, then traveled with Tony to Italy and went to Wyndham’s university lecture.
  • Peter followed Wyndham from the university, placed a tracker on his car, and traced him to his home that night.
  • Peter disabled Wyndham’s security system and began copying files from his computer, but Wyndham spoke up and asked whether Peter planned to leave without saying hello.

Ch. 70Hydra's weapon (4)

Peter stole Wyndham’s files, discovered that Wyndham was keeping Jessica Drew hidden, and fought her before pheromones triggered a powerful mutual attraction. He escaped, but concluded that Wyndham was connected to Hydra and that Peter’s parents had worked for the organization, leaving him to face a dangerous new phase of his life.

  • Peter finished copying Wyndham’s files and overheard Wyndham arguing with a young woman he called his responsibility.
  • The woman sensed Peter, attacked him, and chased him into the woods after he escaped through a window.
  • Peter recognized the woman as Jessica and realized their shared powers seemed to trigger overwhelming pheromone-driven attraction.
  • Peter broke away after remembering Felicia, shocked Jessica with bioelectricity, and escaped without being pursued.
  • While waiting for Tony to send help, Peter suspected Wyndham was with Hydra and that his parents had once worked for Hydra.

Ch. 71Attacking Hydra (1)

Peter and Tony searched Wyndham’s files for evidence connecting him to experiments on children and found an encrypted Super Soldier Serum file that needed missing data to open. After Peter told Felicia the truth about his powers and what happened with Jessica Drew, they discovered that a file from his father’s school papers completed the encrypted data and revealed a Hydra emblem, leaving Peter determined to give the hard drive to Fury.

  • Peter and Tony searched Wyndham’s files but found no evidence linking him to the New York experiments, while Tony discovered a damaged Super Soldier Serum file that needed another half to open.
  • Peter returned home, told Uncle Ben and Aunt May a cover story, and compared Wyndham’s data with his father’s files in the basement lab.
  • Felicia visited Peter, and he confessed the truth about his powers, his search in Italy, and Jessica Drew’s kiss; Felicia forgave him and accepted his explanation.
  • Peter showed Felicia the files, and she noticed a corrupted folder of his father’s school papers that completed Tony’s encrypted ghost drive file.
  • Peter saw a Hydra emblem appear on the screen, destroyed the computer and disconnected the router, then decided to take the hard drive to Fury to protect his family and friends.

Ch. 72Attacking Hydra (2)

Peter and Felicia brought Peter’s parents’ Hydra-linked research drive to Fury, then returned to Queens, where Peter sensed Jessica Drew and tried to escape with Felicia. Jessica attacked Peter in the parking lot, and they faced off while he struggled against an overpowering urge toward her.

  • Peter and Felicia landed on the Helicarrier, where Peter gave Fury the hard drive and warned him that a virus would destroy it if anyone tampered with the data.
  • Peter told Fury that his parents had researched a project connected to Hydra, and he worried that Fury’s agents might discover it involved the Super Soldier Serum.
  • Peter and Felicia went shopping and watched a romance movie at the mall.
  • Peter sensed Jessica Drew nearby and, overwhelmed by lust, tried to leave with Felicia before she reached them.
  • Jessica lunged at Peter in the parking lot, and after he shoved Felicia out of the way, the two fought face-to-face.

Ch. 73Attacking Hydra (3)

Peter fought Jessica and revealed Wyndham’s crimes, but Jessica escaped after attacking him and Felicia. Peter discovered Wyndham had abducted Aunt May and Uncle Ben to demand his father’s research, so he and Felicia set out to rescue them.

  • Peter hurled Jessica across a parking lot, and Felicia blasted her with a blue energy beam.
  • Peter told Jessica that Wyndham had killed thirty-one children while trying to replicate their powers, and Jessica attacked him before fleeing from Felicia.
  • Peter realized Wyndham might have tracked them through the hard drive and rushed home, where he found Aunt May and Uncle Ben missing.
  • Wyndham called Peter, revealed he knew Peter was Spider-Man, and demanded his father’s research in exchange for Aunt May and Uncle Ben’s lives.
  • Felicia insisted on joining Peter to rescue them, and Peter agreed after asking her to stay safe.

Ch. 74Attacking Hydra

Peter stole his father's Super Soldier Serum research from S.H.I.E.L.D. after revealing that Hydra had kidnapped his uncle and aunt, then exchanged the drive for what he believed were his relatives at a construction site. He discovered the captives were decoys, and after binding Jessica, he faced Wyndham's threat against his family.

  • Peter and Felicia stole the hard drive from the Helicarrier, then escaped Captain America, Black Widow, and Hawkeye with Johnny Storm's help.
  • Peter told the Avengers that Hydra had kidnapped his uncle and aunt and demanded his father's Super Soldier Serum research.
  • Peter met Wyndham at a construction site and handed over the hard drive in exchange for his uncle and aunt.
  • Peter discovered the bound figures in the truck were mechanical decoys and charged at Wyndham.
  • Jessica attacked Peter, but he suppressed his desire for her and trapped her with webbing as Wyndham threatened his family.

Ch. 75Hydra's mistake

Peter and his allies fought Wyndham and Sandman, then followed the scientist’s tracker toward the Treadstone black site to find Peter’s aunt and uncle and recover a hard drive. As the assembled teams prepared for an assault, Felicia recognized the mysterious thief Fury brought aboard as her father.

  • Peter, Johnny, and Felicia fought Sandman, Wyndham, and Jessica Drew at the construction site, and Wyndham escaped with the sand while Peter secretly tracked him.
  • Fury learned Wyndham was heading to Treadstone and called in the only thief who had infiltrated its underground base; Peter brought in the X-Men as backup.
  • Jean reunited with Peter and Felicia, while Captain America recognized Logan as James Howlett, though Logan had lost his memories.
  • Jean calmed Jessica, and Fury showed her evidence that Wyndham had killed thirty-one children using her blood; Peter freed her and asked her to help stop Wyndham.
  • Natasha brought Fury’s special asset to the plane, and Felicia and Peter were stunned when she recognized the white-haired man as her father.
Arc 3 of 11
Arc 3 of 11