Where does the MiG-29 store fuel?
Like every plane, the MiG-29 stores its fuel in fuel tanks ;)

On a more serious manner:

Generally speaking, there are 6 internal fuel tanks: 4 distributed around the fuselage and 1 in each wing. 

Later versions (namely the SMT) have larger internal fuel capacity thanks to the enlarged spine.

The exact locations of these tanks can be seen in this cutaway (src): 63, 72, 93, 107, 187.

In addition to these, the 29 can also carry 3 (1 in the very early versions) jettisonable external fuel tanks.