Straczynski's run focused on an alternate timeline created by the Gods where Paradise Island was destroyed leading to many Amazons being raised in the outside world. It revolves around Wonder Woman's attempts to restore the normal timeline despite the fact that she does not remember it properly. Wonder Woman in this alternative timeline has been raised in New York City as an orphan and is coming into her powers. She is aware of the presence of Amazons, but does not remember her childhood on Paradise Island. Wonder Woman wore a new costume designed by DC Comics co-publisher Jim Lee. Writer Phil Hester continued the storyline.
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.
In 1954, Dr. Fredric Wertham alleged that there were lesbian subtexts to Wonder Woman and claimed comics contributed to juvenile delinquency in his book Seduction of the Innocent where despite a very obvious heterosexual relationship with Steve Trevor, Wertham asserted that Wonder Woman’s association with the Holliday Girls could be interpreted as a lesbian relationship. The Comics Code Authority was then introduced in reaction to Wertham 's claims against the entire industry.
Hermes attacked Wonder Woman there, refusing to simply give up the child, but during their battle, War ripped the baby from Demeter's womb and disappeared. Unable to let a grave wound such as that go unattended, Diana saw to Demeter first, and the goddess warned that War could not be trusted. Worriedly, Diana and Orion returned to Manhattan to find that War had returned the baby to Zola. At last, the baby and his mother were reunited - and Orion would not have to look any further for the child he needed to kill.