At about the same time as these political events, an important change took place within the royal family. Nefertiti had so far produced six daughters, but no son, and, although she never lost her prime position as ‘great royal wife’, a second wife of Akhenaten had appeared on the scene at Akhetaten. It has often been speculated that she was a Mitannian princess, but her name Kiya is a perfectly normal Egyptian one and there is nothing to suggest that she was of foreign extraction. She was given the newly created title ‘greatly beloved wife of the king’, which sets her apart from other ladies in the royal harem, while at the same time distinguishing her clearly from Nefertiti. In or shortly before regnal year 12 she suddenly disappears from the monuments; her name was erased from the inscriptions and replaced by those of Akhenaten’s daughters, most frequently that of Meritaten, and her representations were likewise altered. Since even the funerary equipment prepared for her, including a magnificent anthropoid coffin, was adapted for a different royal person, it is most likely that Kiya at some point fell from grace, perhaps because she had become too much of a rival to Nefertiti after she had borne Akhenaten not only a further daughter, but perhaps also a male heir. There is no hard evidence to support this theory, but a single inscription from about this time mentions ‘the King’s bodily son, his beloved, Tutankhaten’ (the future king Tutankhamun (1336-1327 bc)), who was almost certainly a son of Akhenaten, but not of Nefertiti.
The latter’s influence increased even further during the later part of the reign, when she became the official co-regent of her husband as Neferneferuaten with the throne name Ankh(et)kheperura; her role as queen consort was taken over by her eldest daughter, Meritaten. What prompted Akhenaten to appoint a co-regent, a step taken only in exceptional circumstances, is unknown. Perhaps opposition to his regime elsewhere in the country (that is, in Thebes) was threatening to get out of control, making it necessary to have someone who could act as king and perhaps even take up residence outside Amarna; at any rate, a Theban graffito dated to her regnal year 3 reveals that Neferneferuaten owned a ‘Mansion of Ankhkheperura in Thebes’ that employed a scribe of divine offerings of Amun, a clear indication that an attempt at reconciliation with the old cults was undertaken. Most of this text consists of the scribe’s prayer to Amun, with a poignant appeal to the god to come back and dispel the darkness that had descended upon his followers.
Whether or not Nefertiti survived Akhenaten, who died in his year 17, is uncertain. An ephemeral king Smenkhkara with virtually the same throne name as Nefertiti/Nefemeferuaten appears in some inscriptions from the end of the Amarna Period; in one or two rare representations he is accompanied by his queen Meritaten. The identity of this Smenkhkara is uncertain. Many scholars continue to see him as Nefertiti’s male successor, perhaps a younger brother or even another son of Akhenaten, but there is a strong possibility that ‘he’ was actually none other than Nefertiti herself who, like Hatshep-sut before her, had assumed a male persona and ruled alone for a brief period after the death of Akhenaten, with Meritaten in the ceremonial role of‘great royal wife’. Akhenaten’s successor probably did not survive him for very long, and, when he/she died, the very young Tutan-khaten, the only remaining male member of the royal family, mounted the throne. Early in his reign he and his queen, his half-sister Ankhesenpaaten, abandoned Amarna and restored the traditional cults. With him, one of the most incisive periods in Egyptian history came to an end.