But the radical new religion came crashing down with Akhenaten's death. Aten's temples were razed and Egyptians once more worshiped a full pantheon of favored gods.
The Amarna era ended with the disappearance of the royal family's mummies, leaving an enduring mystery for scholars.
"There are probably as many theories about what's going on in the Amarna period as there are Egyptologists who have taken an interest in that period," said Aidan Dodson, an archaeologist at the University of Bristol in England.
The newly scanned mummy's tomb held some clues, however.
The face and cartouche, or nameplate, of the mummy's coffin had been hacked out. But traces of gold leaf, along with hieroglyphics surrounding the cartouche, hinted over the years that the body might belong to the heretical leader.
"I think the alteration of the coffin in KV 55 suggests it must be a male member of the Amarna royal family and most likely Akhenaten," said Peter Lacovara, an archaeologist for the Amarna Royal Tombs Project, which is affiliated with England's Durham University.
The CT scan supports the idea that the mummy is Akhenaten by revealing it as a male between the ages of 25 and 40 who shares many physical similarities with Tut—assuming Akhenaten was Tut's father, as some experts believe.
The mystery mummy's strange elongated, egg-shaped skull, called dolichocephalic, is strikingly similar to Tutankhamun's.
The jaw, cheekbones, cleft palate, impacted wisdom teeth, and slight scoliosis of the spine are all also similar to Tut's—suggesting familiar traits that may have been passed on from father to son.
"[This] means we can say now the mummy in KV 55, based on this evidence, and based on the age, and based on the inscriptions written in the coffin, that this could be the mummy of Akhenaten," Hawass told the National Geographic Channel.
But the mummy could also be one of several other people—including another mysterious member of Tut's family—Hawass cautioned.
Dodson, of the University of Bristol, said, "I still think that the mummy is that of Smenkhkare—who was probably either the brother or son of Akhenaten and thus will have shared many of his features."
"Akhenaten may have been buried at one time in KV 55—'magic bricks' [denoting a royal tomb] in his name were found—but the mummy was probably later removed and destroyed. I do not believe that there will ever be 100 percent agreement about this particular mummy."
Even ascertaining the family trees of ancient Egypt's dynasties can be difficult, Dodson added.
"The concept of a royal family recording who was the son of whom just didn't happen," Dodson said.
"There's virtually no example of [recorded evidence for] a king being the son of his predecessor until the 19th dynasty [around 1290 B.C.]. Until then the royal sons are hardly ever mentioned on monuments at all."
No Clues on Nefertiti
The research expedition originally centered on Akhenaten's better-known wife—Nefertiti. But her whereabouts remain unknown, the team says.
Two female mummies found together just a few hundred feet from King Tutankhamun's burial chamber have been the focus of endless speculation.
At various times both corpses, known as the "Younger Lady" and the "Elder Lady," have been identified as the queen—but none of these assertions has proved conclusive.
CT scans revealed critical new information about these mummies, including the women's ages at death, their history of childbirth, the nature of wounds, important piercings, and the original positions of their arms—a key indicator of royal status.
The cumulative evidence led Hawass's team to conclude that neither is Nefertiti.
"The [Younger Lady] mummy that everyone thought is Nefertiti, it is not Nefertiti," he told the National Geographic Channel. "We gave the proof for that."
The Elder Lady may be the powerful Queen Tiye, Akhenaten's mother, while the Younger Lady might possibly be his secondary wife Kiya—the likely mother of King Tutankhamun—the researchers say. (Related: "Egypt's Female Pharaoh Revealed by Chipped Tooth, Experts Say" [June 27, 2007].)
DNA evidence is probably the only way to provide definitive identifications, but it may be impossible to acquire after so many years.
So Nefertiti may remain lost forever, said Lacorva, of the Amarna Royal Tombs Project.
"Barring any significant discovery, such as her burial, which is unlikely," he said, "we may never know the truth."
A one-hour special on the mummy investigation, Nefertiti and the Lost Dynasty, will air on the National Geographic Channel Monday, July 16, at 9 p.m.
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