Creepy undercurrent to the movie knowing the giant is a weapon likely created by alien colonists

Same with "Lilo and Stitch", which as the same plot (but which came several years later). A simple story of friendship and redemption, with the undercurrent of danger because one of the friends is a killer alien who answers to no human law.

The undercurrent of danger is much stronger in "Iron Giant", which is one of the reasons it's a better film.