Thomas Anderson, a.k.a. Neo (Keanu Reeves) has been having dreams that are visions of the past. When he encounters Trinity (Carrie-Anne Moss) at a coffee shop, they feel as if they know each other. The meeting triggers something in Neo, and after he downs a blue pill, he encounters a person (Yahya Abdul-Mateen II) who has all the answers he's seeking.

Neo and Trinity have returned to the Matrix after seemingly dying after the war with the machines, but must now figure out how and why.