Gwen's father Captain Stacy expressed his discontent for her activities as Spider-Woman and informed her he was replaced with the NYPD's tough-as-nails cop Frank Castle (aka the Punisher) on the vigilante investigation. During their conversation, Vulture attacked with gas incapacitating Gwen's senses. She followed him only to clash with Castle who unmasked her. To his shock that she was "just a girl" she rebounded and escaped his grasp.
She continued to save people but experienced a lot of distrust. Simultaneously, she struggled with the loss of Peter and having to face his Uncle Ben and Aunt May. When May expressed that she noticed Spider-Woman trying to help after Peter died, Gwen regained some faith in her crime fighting endeavors and rejoined her band. During an attack on Murdock at one of the band's shows, Murdock admitted his involvement in Vulture's attack on Captain Stacy and implied knowledge of Spider-Woman's identity.
When the Multiverse was destroyed, Gwen ended up on a patchwork planet known as Battleworld led by Mayor Norman Osborn. Her memories muddled, she fought crime as Spider-Gwen on this new world. Working alongside Spider-Totems from other worlds, Gwen joined them against the Sinister Six, they defeat Osborn and protect the Web of Life and Destiny. They called themselves the Web-Warriors and use their powers to fight for the fallen.
Gwen returned to Earth-65 and discovered the reappearance of the Lizard, making her doubt whether Peter Parker died. She uncovered that the real culprit was Dr. Curtis Connors and one of many other lizards. She battled them only to be arrested by S.H.I.E.L.D.'s representative Samantha Wilson/Captain America.
Gwen travelled to Earth-616 to learn about her counterpart and encountered Jessica Drew (Spider-Woman), who reminded her about lessons in responsibility. She returned to her Earth and found Harry Osborn had come back from the army and equipped with S.H.I.E.L.D. training. He revealed his vendetta against Spider-Woman for killing Peter.
Osborn consumed the same serum that Parker had and with increased strength, he unmasked Spider-Woman to reveal his friend Gwen. Captain America intervened but it was Gwen that ultimately halted the Green Goblin's revenge plot and offered him a second chance. In working alongside Captain America, she gained an ally.
Meanwhile, Gwen's father Captain Stacy still struggled with her double life but he eventually came to terms with it and quit his job to focus on being her dad.
Spider-Gwen then fought alongside Silk and a visiting Earth-616 Spider-Woman against Cindy Moon. Moon revealed she had created the spider that gave Spider-Gwen powers and then injected her with a formula which removed them. A former S.H.I.E.L.D. agent Jesse Drew, who worked with Moon, defected and helped Spider-Gwen restore her powers temporarily.
While she battled the imminent loss of her powers, she reconnected with her friends. Castle, now knowing her identity, attacked her. Spider-Gwen was saved by her father, but he only temporarily protected her as Castle was unstoppable. He mounted another attack to kill Gwen but was halted when he turned himself in to the cops, admitting that he aided and abetted Spider-Woman.