Years before the Battle of New York and before the Avengers ever assembled, Clint Barton and Natasha Romanoff undertook one mission that never appeared in any S.H.I.E.L.D. file. Sent to recover a classified intelligence archive known as the Janus Protocol, they discover that it is capable of exposing every undercover S.H.I.E.L.D. operative around the globe. After discovering that powerful figures across the world's intelligence agencies intend to weaponize the information rather than destroy it, Clint and Natasha fake the mission as a failure and hide the drive before anyone can find it. Only the two of them know where the secret died...until Natasha's sacrifice on Vormir leaves Clint as its sole guardian.
Years later, someone uncovers clues leading to the Janus Protocol. Fifteen years later, Natasha is gone, Clint has retired, and a new threat emerges. Criminal mastermind Madame Masque begins hunting the lost archive, forcing Kate Bishop and Yelena Belova to finish the mission that Clint and Natasha never could. As the film shifts between timelines, the audience watches the legendary partnership of Hawkeye and Black Widow while seeing their legacy live on through the next generation.