RE: Top sights and how to get there!
When are you going?
If you're there in the winter, the ski resort, Snowbowl, may be open. In the summer, the ski resort just runs the lift up to the second highest peak in AZ, which is a real nice site. There's no public transit up there as I understand it (a bus comes by the base though), but you could probably bum a ride off of someone if you ask around. People in Flag are incredibly friendly, provided you're non-threatening.
Flagstaff's bus system is called the Mountain Line (get it?):
There's also the Museum of Northern Arizona, which is nice. A bus will take you there. Flagstaff is also surrounded by National Forest land, and there are plenty of hikes that start close enough to the city that you could take a bus to the trailheads.
Just outside of the city, there's the Lava Tubes, Lockett Meadow, Wupatki/Sunset Crater NM and Walnut Canyon NM, but I don't believe any are serviced by public transit, and Lockett Meadow is several miles off the main road.
The main attraction in Flag though is its Downtown. You could spend quite a bit of time there.
There are also tours that leave for Sedona, Monument Valley, the Navajo Reservation, Petrified Forest, etc, but these, of course, cost quite a bit.
Hope that helps.
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