Possible Clues:

• Hit sci-fi film with Keanu Reeves
• Hit film of 1999
• Famous trans allegory in film
• Keanu film franchise
• Hit 1999 film that popularized a slo-mo effect known as 'bullet time'
• Place explored in a 1999 film (and the 2003 theme of the 39-Across)
• Movie with the line "There is no spoon"
• Movie with a red pill and a blue pill
• 1999 sci-fi film