When there is a ruckus outside the church there are the options to hide in the church, stay and watch what happens, or to leave. If you leave, you'll be in the place to start Oleander and Francesco's routes!
If you don't have the option to leave then you're playing in an old version of the game and will need to download the updated version. You'll keep your saves and unlocked endings and CGs when you download the new version. We do recommend starting Francesco and Oleander's route from a fresh start, though, to avoid any possible bugs.