Spoilers for Avengers 1,000,000 BC by Marvel Comics
After months of teasing that Thor was somehow the son of the first Phoenix, Marvel Comics has revealed the truth behind the God of Thunder's parentage. In Avengers 1,000,000 BC, Thor's birth parents don't change from his classic origin, as Odin and Gaea are his biological father and mother. However, the Phoenix played a key role in keeping Thor alive, resulting in the future Avengers' connection to the all-powerful entity.
In the current ongoing Avengers series from Marvel Comics, readers were shocked to learn that the first Phoenix on Earth was somehow Thor's biological mother. Originally the son of Odin and Gaea, the Phoenix Force claimed Thor as her own - which was a considerable retcon from the character's classic origin. After teasing Thor's secret history for months, Marvel finally revealed the truth behind the God of Thunder's parentage; as it turns out, he's still the son of Gaea, but the Phoenix Force played a crucial role in ensuring he survived a deadly attack as an infant.
In Avengers of 1,000,000 BC by Kev Walker, Jason Aaron, Dean White, and VC's Cory Petit, Thor's Phoenix origin is revealed. In the story, Odin attempts to woo the Phoenix, making a move on her following the death of the Black Panther. Phoenix wants nothing to do with Odin, demanding he shows respect - while she considers destroying the Earth for its primitive nature. Meanwhile, Gaea, who developed a friendship with the Phoenix, gives birth to Thor, but after he's hit with the blade of a Frost Giant, he's turned into ice. The Phoenix breathes the fires of life back into the infant, which explains how the God of Thunder is connected to the Phoenix Force in the present day.
The issue ends up doing a tidy job at explaining how Thor is the "son" of the Phoenix, without changing his biological parents, Odin and Gaea. The Phoenix helped an infant Thor and used her life-bringing powers to save his life. It explains how Thor got his Phoenix powers without damaging the previously established canon.
Gaea and later Freyja are still the mothers of Thor. But, thanks to the first Phoenix's intervention, the hero's origin will now forever be tied to the fiery being. Without the Phoenix, an infant Thor would likely have died in the battle against the Frost Giants. Ultimately, even if she isn't the biological mother of Thor, without the Phoenix, he would have never become the God of Thunder. Avengers 1,000,000 BC from Marvel Comics is in comic book stores now.