Trying to remember a movie where a modern ship (submarine or carrier?) goes into a storm and ends up in WWII battle.

Might be 1980's The Final Countdown (http://www.imdb.com/title/tt0080736/), where a modern American aircraft carrier timewarps back to just before the attack on Pearl Harbor.

Definitely "The Final Countdown" but the American jets never actually made get into a large-scale battle with the Japanese prop planes as they have to get back to the carrier before the storm hits again which takes them back to present day.