Resident Evil Village picks up roughly three years after the events of Resident Evil 7, with Ethan and Mia Winters starting a new life in Europe. The game's marketing started off with a bang, literally, when the first Resident Evil Village trailer showed series protagonist Chris Redfield murdering Mia Winters.
[WARNING: Spoilers for Resident Evil Village's ending below]
The opening of Resident Evil Village also features this scene, then unceremoniously dumps Ethan in the mysterious, titular village. Resident Evil games have always had plenty of mysteries and twits, and the newest game is no different. Later in Resident Evil Village's story, Chris' motivations become abundantly clear, and the opening events and questions surround why he shoots Mia are put into context.
Mother Miranda is the true villain of Resident Evil Village, but players don't actually interact with her until near the end of the game. After Ethan defeats Heisenberg, he's confronted by Mother Miranda, who reveals that she has the power to impersonate any person, and she took on the role of Ethan's wife Mia.
Chris Redfield's Real Role in Resident Evil Village
When Chris and his squad infiltrated the Winters' house at the beginning of Resident Evil Village, they were actually trying to execute Mother Miranda - and did so with extreme prejudice. Unbeknownst to Chris, however, Mother Miranda possesses the ability to simulate her own death, and did so in order to trick Chris' squad and kidnap Rosemary Winters, Ethan's daughter. It's not exactly clear when Mother Miranda took the place of Mia Winters, but she kidnapped the real Mia in the process.
Luckily, Mia is still alive and imprisoned in Mother Miranda's laboratory in the village. She's eventually rescued by Chris Redfield as he fights through the embattled village, searching for Miranda. Mother Miranda's ultimate plan is to use Rosemary to revive her daughter Evelyn - the same Evelyn that was the bioweapon behind the events of Resident Evil 7. All of the experiments in the village were Mother Miranda trying to find a proper vessel to reincarnate Evelyn, but she could never find a suitable subject until she learned of the Winters' daughter.
Rosemary has a unique connection to Evelyn because of her parents, especially through Ethan thanks to the genetic material that was injected into him in Resident Evil 7. It's a little convoluted, but it basically boils down to the fact that Mother Miranda was the one responsible for everything, both the events of Resident Evil 7 and Resident Evil Village, and that's who Chris was really shooting.