We'll zap the ship with a time-moving device that sends it 3,333 years back in time.

It will pop out of nowhere making a bridge across the Red Sea, just as the Israelites need to cross it. They will.

When the Egyptians run across it as well, we'll find out the time moving device was temporary, and the ship reappears in the present time (hopefully at sea or at a better angle).

The Egyptians fall into the ocean and drown.

The Israelites decide the story of what really happened is too far fetched, so they write down the more plausible story that the ocean merely split in two.

(Now really hoping I don't get hit by a lightning bolt for this)