Lets do a little bit of theorizing.
Season 2 of Good Omens had an open ending, so Neil Gaiman was clearly working on that part with the intention of doing a season 3 in the future.
In the season 2 finale, the Metatron invited Aziraphale to become the new leader of Heaven and work on the Second Coming project — whatever that might mean. Aziraphale agreed to go to Heaven, while Crowley stayed on Earth.
Season 3 hasn’t been confirmed yet, but fans already have theories about what secrets it will reveal.
1. Сrowley will no longer be a demon
There is a popular theory in the Good Omens fandom that Crowley will return to his angelic form in the third season.
Some eagle-eyed fans have noticed that Crowley’s eye color changes throughout the series. At first, his eyes are completely yellow and snake-like, but then they become almost completely human-like. Neil Gaiman has confirmed that this change is intentional.
Perhaps thanks to Aziraphale, Crowley will change for the better?
2. The Coffee Theory
In the second season, the Metatron invited Aziraphale to lead Heaven, he first refused, but later agreed after having a sip of his coffee. Fans have theorized that the Metatron did something to the coffee to get Aziraphale to accept his offer.
Before meeting Aziraphale, the Archangel went to the Give Me Coffee Or Give Me Death cafe and asked the owner, Nina, if any of the customers were asking for death. Nina replied that everyone only ordered coffee. With this question, the Metatron implied that the name of the cafe did not give customers the right to choose – it was unlikely that anyone would prefer death.
By asking about the name of the cafe, the Metatron probably meant that Aziraphale didn’t really have a choice, too, but we’ll find out if that’s true in season three.
3. Aziraphale is the one responsible for Crowley’s exile from heaven
One of the biggest mysteries of the show is why Crowley was kicked out of Heaven. A popular fan theory is that Aziraphale is the one to blame.
Flashbacks have shown that Aziraphale was concerned that Crowley was questioning God’s plan, and he may have had the best intentions of reporting this to the Metatron, which could have resulted in Crowley’s exile.
Fans believe the showrunners will reveal this secret in the third season.
4. The Metatron is the real villain
The Metatron is introduced in the second season and is essentially the voice of God. He is an authority in Heaven, an important part of the Creator, but also a sort of separate being.
The Metatron raised suspicions among fans at the end of the second season. His behavior was not that of someone who came with good intentions. Now many fans believe that he will become the main enemy and villain of the third season.
