It's a pretty basic story about a boy practicing the arts of ninjutsu, fighting evil and trying to find his mother. 
Young Fujimaru got snatched away from his mother by an eagle and was rescued by a ninja named Sasuke who raised him and taught him ninja techniques. 
Later Fujimaru embarks on a quest to find his mother, encounters his arch enemy and learns about a secret book that contains secret ninja arts. 
The series is pretty old, but portraits loads of classic ninja techniques, like elemental manipulation (fire &amp; wind), creating illusionary clones and breathing through a reed.