Place rich in history, better have a read before visiting, otherwise it's just going to be an unfinished building for you. It was supposed to be an enormous pagoda, imagine how massive it would've been if finished.
There’s a museum just next door to the mission, the Museo de los Misiones (tel. 613/135-0441, open 9a.m.-1p.m. and 1:45p.m.-6p.m. Tues.-Sun.) run by INAH. The small museum has some interesting exhibits about the history of the missions and the missionaries including historic maps and artifacts from daily life during that era.
The caretaker of the mission is a fourth generation Cochimí (one of a handful of native tribes in the region) and he and his family give free tours of the mission from 8a.m.-6 p.m. daily. Behind the church are adobe ruins of earlier constructions.
Don’t visit the mission at San Javier without taking some time to walk around the back of the mission, exploring the old gardens of the mission and stopping to see the large gnarled olive tree that’s over 315 years old.
Just to the left of the mission, the Instituto Nacional Antropología e História (INAH) has a small museum (open 8 a.m.-6 p.m. Mon.-Sat.) with some history of the region and information about the rock art of the Sierra de San Francisco.
Be sure to walk around the back of the mission where you’ll find steps up to a small mirador lookout that offers great views of the Río Santa Rosalía (the Mulegé River) and of town. Please note that there’s sometimes an aggressive swarm of bees at the lookout. Be careful if you’re allergic.