The Phoenix Force is a force of the universe that creates all life. From the birth of the universe, she began creating stars, planets, even lifeforms. But when those lifeforms advanced in technology and civilization, they became jealous of the Phoenix and rose up to capture and control her. After millennia of fighting, her creations found they could only imprison her, not kill her. Unfortunately, they could not hold her with conventional means and thus used any amount of matter to create the planet Earth.
Church of Shi'ar Enlightenment
A human cult, known as the Church of Shi'ar Enlightenment, began to worship the Phoenix and worked to release her from her earthly prison. They theorized that the Phoenix was located at the center of the core and was responsible for the creation of human life and the mutants. However, a splinter group, believing the Phoenix to be a being of destruction, became the Hellfire Club.
The Church approached Charles Xavier with the proposal of giving funding after he lost government support in exchange for testing on Jean Grey, who they believe to be the avatar and/or host of the Phoenix. But when the Phoenix arose in the young mutant near her twentieth birthday, wanting to unleash her anger upon all mortals. Xavier managed to shut off her brain before she could melt his.
Afterwards, tests made by Lilandra Neramani's assistant Gerald says that the Phoenix that awoke in her was false. But Gerald had lied and was actually working for the Hellfire Club as the tests were positive.
Rise of Apocalypse
When Apocalypse is about to kill Xavier in the future, Jean calls out to the Phoenix, who merges with her body. Together, they defeated Apocalypse and revert him to his Sinister form.
Just before burying the many mutant victims of the Ultimatum, Jean Grey reveals that she is no longer the Phoenix. She can no longer manipulate space and time. The only explanation she gives is that she has "been punished", has "wasted it", is "selfish" and "unworthy".
When attempting to coerce Kitty Pryde into allying with Tian, Jean suddenly unleashes the power of the Phoenix, creating a fiery Phoenix raptor around herself. It appears Jean has somehow regained the power of the Phoenix after apparently losing it.