Complex sentence: The Jesuit missions in Baja California were then turned over to the Franciscans, and the future missions in Alta California--which would otherwise have become Jesuit institutions--were founded by Franciscans.
Split into simpler sentences: The Jesuit missions in Baja California were then turned over to the Franciscans. So the future missions in Alta California--which would otherwise have become Jesuit institutions--were founded by Franciscans.