The Final Countdown/WMG

Despite the awesomeness of of the armada of modern aircraft moving to intercept the Japanese fleet, they would have been destroyed or failed for some reason to preserve the time stream.
Two people left behind is one small thing - a huge event like preventing Pearl Harbor would have been catastrophic. Maybe a Japanese submarine would have sunk the Nimitz with an incredibly lucky shot. Maybe a freak up/downdraft would have sent all the planes into the ocean.
 * No 'incredibly lucky' shot required -- the Nimitz was sailing without its ASW escorts, which meant it was dead meat for any submarine that happened by.

The storm returned because they were about to commit a huge change on the time line.
The Nimitz inadvertently invoked the circumstances for them to return home.

The Nimitz was Doc Brown's prototype
He decided that a DeLorean would be a better idea.