Earth Shining There (not sure if this is the correct translation)

This short film was made in the early 2000's. It opens with a boy being chased by robots into a museum where he discovers the deactivated body of Atom hanging in a display case. Due to the actions of the robots chasing the boy, or an electrical storm raging outside of the building, a bolt of lighting sets off an explosion in the display area, knocking Atom over and reactivating him. Atom saves the boy from his pursuers, only to run out of power.

The boy manages to carry Atom to a waiting submarine where an older version of Dr. Ochanomizu is waiting. It appears that he is the boy's guardian. The submarine is then chased by robots that look like they came right out of the Matrix. Eventually they confront an A.I. that seems to be in control of the robots, at which point Atom wakes up from a dream back in the early 21st century with Uran and Dr. O'Shay.

(more editing required)