After Darkseid and Grail's retreat, they returned to a base in the Amazon Rainforest, where Darkseid was setting his mysterious plans into motion. He tasked his loyal Female Furies with tracking down a godly relic he needed, but they were unable to do so thanks to the intervention of Steve Trevor and his A.R.G.U.S. forces. Meanwhile, Wonder Woman fought a number of villains that had been recruited by Veronica Cale: Zara of the Crimson Flame, Blue Snowman and Anglette. As Diana caught up with Steve at A.R.G.U.S. HQ, Jason returned wearing a suit of armor gifted to him by the gods, but with no knowledge of its purpose. As news came in of an attack by Grail, Wonder Woman and Jason immediately responded just in time to prevent Grail from killing another demigod. Wonder Woman bound Grail in the Lasso of Truth and forced her to reveal Darkseid's plans. Grail explained that Darkseid was looking to build himself an army of Amazons. Due to her half-Amazon blood, Grail was able to break free from the Lasso's grip and retreated.
The Crisis on Infinite Earths crossover of 1986 was designed and written with the purpose of streamlining most of DC's characters into one more-focused continuity and reinventing them for a new era, thus Wonder Woman and Steve Trevor were declared to come from the Earth-Two dimension, and along with all of their exploits, were erased from history, so that a new Wonder Woman character, story and timeline could take priority.
Lennox suggests meeting Siracca, a fellow demigod daughter of Zeus as well. She travels to Lybia and finds a girl trapped in a vase. The girl tells Wonder Woman that when the soldiers came, everyone hid in a bunker. Leading her down, she triggers a trap which sends a plethora of knives, swords and daggers at her. Blocking them all but one, Diana looks to find the girl dissolving to sand. Crying at her failure, her time to mourn is cut short as the real Siracca, albeit in a zombie like form, ambushes her.
Wonder Woman appears in the first three issues of the Ame-Comi comic run. She is depicted as a young warrior eager to prove herself in battle, but when she goes against her mothers words it results in a punishment of sorts. Diana is made into an ambassador of peace to the world outside of Themyscira, which she is reluctant to perform. At a U.N. Assembly where she announces Themyscira's intention for peace she is attack by Cheetah, who is quickly defeated. This depiction of Diana is that of a younger amazon who is depicted in a more arrogant and aggressive manner.
Starting in Wonder Woman vol. 2 #51, the Amazons, who had revealed their presence to the world in Wonder Woman vol. 2 #50, are blamed for a series of murders and for the theft of various artifacts. The Amazons are then taken into custody, Queen Hippolyta is nowhere to be found and Steve Trevor is forced by General Yedziniak to attack Themyscira. These events lead to the "War of the Gods" occurring. The culprit of the murders, thefts and the framing of the Amazons is revealed to be the witch Circe, who "kills" Diana by reverting her form back into the clay she was born from. Later, Wonder Woman is brought back to life and together with Donna Troy, battles Circe and ultimately defeats her. Circe would later return by unknown means.
The final remaining relics Darkseid needed were being guarded by A.R.G.U.S. at their HQ, so Darkseid decided to use a Boom Tube to transport the building and all its contents to his base in the Amazon Rainforest. The Female Furies retrieved the relics and put them into place while Wonder Woman fought Darkseid. With the relics' power, Darkseid was able to open a portal to Themyscira. As it is impossible for one who has set foot on Themyscira to return after leaving, Diana was unable to follow Grail through the portal. Grail invaded and began transforming the Amazons into creatures resembling Darkseid's Parademons. As Jason had never actually set foot on Themyscira, he followed Grail and met his mother Hippolyta for the first time since his birth. While Jason and Hippolyta fought off the transformed Amazons, Wonder Woman was able to defeat Darkseid through her love for her deceased father, Zeus, and her half-siblings, calling their spirits out of Darkseid's body and destroying him from the inside. The Amazons captured Grail and imprisoned her in the prison beneath Themyscira, alongside Ares, while Darkseid re-emerged somewhere on Earth. Jason was gifted a magical spear from his mother and returned to Earth.
Now a mod boutique owner, the powerless Diana Prince acquired a Chinese mentor named I Ching. Under I Ching's guidance, Diana learned martial arts and weapons skills, and engaged in adventures that encompassed a variety of genres, from espionage to mythology. During this time she fought villains such as Catwoman, Doctor Cyber, the hippie gang Them!, and the campy witch Morgana.
John Byrne's run included a period in which Diana's mother Hippolyta served as Wonder Woman, having traveled back to the 1940s, while Diana ascended to Mount Olympus as the Goddess of Truth after being killed in issue #124. In addition, Wonder Woman's Amazon ally Nubia was re-introduced as Nu'Bia, scripted by a different author. Byrne posited that Hippolyta had been the Golden Age Wonder Woman. Byrne restored the series' status quo in his last issue.
Zeus has made a woman called Zola pregnant. Hera, due to this, is furious. She sets out to kill Zola, but Hermes finds her first, only to find out that Zola does not want to come with Hermes. Zola opens the door, and an arrow is shot at her direction; Hermes pushes her away in time, and gives her a key, as assassins sent by Hera and it teleports to Wonder Woman’s apartment, because Hermes enlisted Wonder Woman to protect Zola. Zola gives Wonder Woman the key, and it teleports both Wonder Woman and Zola back to Zola’s house. After Zola finds out that she is pregnant with Zeus, it gets revealed that one of Zeus’ children is going to take his place, by Zeus’ own will. Wonder Woman takes Zola, along with Hermes, to Themiscyra where Diana explains to her Mother, Queen Hippolyta, why she took with herself Zola and Hermes to Themiscyra. Alongside all of this, Hippolyta tells Diana about her true origins; that her real father is Zeus. Diana’s reaction to this isn’t very well, so she decides to abandon Themiscyra. Hera is aware of the fact that Wonder Woman is Zeus’ daughter, and she arrives to Themiscyra, furiously. Wonder Woman realized she did a mistake by leaving her home, so she went back to Themiscyra where she sees that everyone has been turned into snakes by Hera, except for Hippolyta, she was turned into stone. Apollo arrives in a bar searching for War (Ares), and explains to him that Zeus doesn’t even exist from what he’s sources says. Apollo takes this as his chance to become the king of Olympus and the Gods.