I want him to have to put something back. It's been 25 years since the Nazi's have discovered Tanis. The Jews returned to their homeland in 1945 and real research had been done on what happened in Egypt all those years ago. Some rogue student that didn't study Michelson is now the Worlds leading living expert on the Ark and finds an ancient text in the Dead Sea scrolls about how stealing something the final resting place of God would be met with apocalyptic cataclysm. This student wants to hasten that, so he sets off to steal the Ark from it's warehouse, and get it to a part of the world that he's deemed needs judgement.
Indy now reluctantly is drawn out of his retirement, because he wants to get the Ark back to Tanis and prevent the whole shebang. It becomes a cat and mouse adventure (with noir elements) to tie the whole thing up and bookend it.