After becoming co-regent, Smenkhare was sent to Thebes in what was believed to be an attempt at reconciliation with the priests there. We do know there was an inscription found in a temple erected in Smenkhare's name at Thebes, which provides evidence of a revival of the cult of Amun. This inscription dates from the third year of Smenkhare's reign, a time when Akhenaten was, quite probably, still alive.

A theory is that Nefertiti disappeared from the scene because of Smenkhare. Given her great beauty, it seems impossible there existed a female who could take her king's attention from her. Therefore, when Akhenaten's eye began to wander, it came to rest on the attractive, and male, Smenkhare. He made the young man his co-regent and bestowed upon him one of Nefertiti's former titles, Neferneferuaten (beloved of Re's One and Only).

The relief that appears above shows Akhenaten and Smenkhare in "scandalous" intimacy - the pair sitting close together, arms around each other, the pharaoh caressing his co-regent; and in other reliefs, even kissing him.

Akhenaten and Smenkhare enjoyed a brief period of rule together before dying, probably within a year of each other. Some hold that Smenkhare died first, others that Akhenaten died first. If Smenkhare did survive Akhenaten and rule alone, it was for a very brief period. Akhenaten was not buried in the massive tomb which was being prepared for him. The only bodies found there were those of his daughter, Meketaten (who died young) and the remains of an unidentified and burnt man found outside the tomb.

Horemhab tried to remove the names and memories of his predecessors so they might "die a second death and vanish forever." He inflicted his vengeance upon the memories of Akhenaten, Smenkhare and Tutankhamun. Thankfully, Horemhab was unsuccessful in his attempts to eradicate the pharaohs from the pages of history.