Her story will be filled in via flashbacks, likely as she recovers from memory loss and reconnects important dots that tell her she had a life here on Earth, before she was blasted by Kree radiation and given the ability to fight in the cosmos.
Marvel President Kevin Feige has said that unlike normal origin stories, Captain Marvel will begin when the main character already HAS her powers.
And from what I know, this will be closer to the beginning of the movie.
There’s also the explosion that will careen Carol Danvers into a Blockbuster Video.