In 2013, when Daily Planet reporter Lois Lane tracked Clark Kent to Smallville. He revealed himself at the cemetery and explained why he didn't want his secret to be revealed. Clark and Martha Kent later came back to visit Jonathan's grave.
Batman came to the conclusion that the Justice League needed Superman if they truly wished to save the Earth. Flash and Cyborg were sent to retrieve Clark's body and bring him to the Kryptonian ship in Metropolis.