Scholars Kenneth Kitchen and Jürgen von Beckerath have theorized that Amenmesse usurped the throne from Seti-Merneptah, who was Merneptah's son and crown prince and who should have been next in the line of royal succession.
Kitchen has written that Amenmesse may have taken advantage of a momentary weakness of Seti-Merneptah or seized power while the crown prince was away in Asia.
Confusion generally clouds Amenmesse's reign and its correct position within the succession sequence of the rulers of the Egyptian 19th Dynasty.
However, an increasing number of Egyptologists today such as Rolf Krauss and Aidan Dodson maintain that Seti II was in fact the immediate successor of Merneptah "without any intervening rule by Amenmesse.
Seti would finally defeat his rival Amenmesse and return to Thebes in triumph whereupon he ordered the restoration of his damaged tomb.
[11] In particular, two representations of Messuy on the temple of Amida allegedly show that a royal uraeus had been added to his brows in a way consistent with other pharaohs such as Horemheb, Merneptah and some of the sons of Rameses III.
An inscription at the temple of Amada also calls him "the king's son himself" but this may be merely a figure of speech to emphasize Messuy's high stature as Viceroy under Merneptah.
Papyrus Salt 124 records that Neferhotep, one of the two chief workmen of the Deir el-Medina necropolis, had been killed during the reign of Amenmesse (the king's name is written as Msy in the document).
If Amennakhte's allegations can be trusted, Paneb had stolen stone for the embellishment of his own tomb from that of Seti II in the course of its completion, besides purloining or damaging other property belonging to that monarch.
[16] His mother is known to be Queen Takhat, but who she is exactly is a matter of interpretation complicated by inscriptions being revised by Seti II and Amenmesse.
[19] Others such as Frank Yurco believe Takhat was wife to Merneptah making the rivals Seti II and Amenmesse half-brothers.
Six quartzite statues originally placed along the axis of the hypostyle hall in the Amun Temple at Karnak are thought to be his, although these were defaced and overwritten with the name of Seti II.
His mummy was not amongst those found in the cache at Deir el Bahri, and from the destruction of his tomb in the Valley of the Kings, it is assumed that Seti II took revenge upon his usurping half-brother.
After his death, Seti II also conducted a damnatio memoriae campaign against the memory of Amenmesse's Vizier, Khaemtir.
The destruction of this figure is likely to have closely followed the fall of Bay or the death of Siptah himself, when any short-lived rehabilitation of Amenmesse will have ended.[28]M.