Meanwhile, the Persian Achaemenid Empire to the east, led by Cyrus the Great, had been gaining strength. King Cyrus had become popular among the residents of Babylon by posing as the one who would restore Marduk to his rightful place in the city. As the Persians advanced to Babylon, Nabonidus returned. He was captured by the Persians in 539 BC and Babylon was occupied, thus ending the Neo-Babylonian Empire. Cyrus was welcomed into the city, where he performed the rites of Marduk. Nabonidus’ fate is uncertain, though it is believed he was exiled to Iran and allowed to occupy a government post.
Modern perceptions of Nabonidus' reign have been heavily colored by accounts written well after his reign as king of Babylon, most notably by the Persians and the Greeks. As a result, Nabonidus has often been described in very negative terms in both modern and contemporaneous scholarship. However, an accumulation of evidence and a reassessment of existing material has caused opinions on Nabonidus and the events that happened during his reign to alter significantly in recent decades.
Nabonidus' background is not clear. He said in his inscriptions that he was of unimportant origins. Similarly, his mother Addagoppe, who lived to an old age and may have been connected to the temple of the moon-god Sîn in Harran, does not mention her family background in her inscriptions. There are two arguments for an Assyrian background: repeated references in Nabonidus' royal propaganda and imagery to Ashurbanipal, the last great Neo-Assyrian king; and Nabonidus' originating from, and his special interest in Harran, an Assyrian city and the last stronghold of the Neo-Assyrians after the fall of Nineveh, their main capital. A few inscriptions name Nabonidus’ father, Nabu-balatsu-iqbi, satrap (governor) of Harran and descendant of Esarhaddon, though one brick inscription from Harran lists his name as “Naksu” in place of “Nabu”. Inscriptions title him as The Wise Prince and The Devotee of the Great Gods and Goddesses, however his family is never mentioned, leading to the assumption he died as a young man.
However, it has been pointed out that Nabonidus' royal propaganda was hardly different from his predecessors, while his Persian successor, Cyrus the Great, also referred to Ashurbanipal in the Cyrus cylinder. He certainly did not belong to the previous ruling dynasty, the Chaldeans, of whom Nebuchadnezzar II was the most famous member. He came to the throne in 556 BC by overthrowing the young king Labashi-Marduk.
Nabonidus took an interest in Babylon's past, excavating ancient buildings and displaying his archeological discoveries in a museum. In most ancient accounts, he is depicted as a royal anomaly. Nabonidus is supposed to have worshipped the moon-god Sîn beyond all the other gods, to have paid special devotion to Sîn's temple in Harran, where his mother was a priestess, and to have neglected the Babylonian primary god, Marduk. He left the capital and travelled to the desert city of Tayma in Arabia early in his reign, from which he only returned after many years. In the meantime, his son Belshazzar ruled from Babylon.
Nabonidus is most revered and is known as the first archaeologist. Not only did he lead the first excavations which were to find the foundation deposits of the temples of Šamaš the sun god, the warrior goddess Anunitu (both located in Sippar), and the sanctuary that Naram-Sin built to the moon god, located in Harran, but he also had them restored to their former glory. He was also the first to date an archaeological artifact in his attempt to date Naram-Sin's temple during his search for it. Even though his estimate was inaccurate by about 1,500 years, it was still a very good one considering the lack of accurate dating technology at the time.
Although Nabonidus' personal preference for Sîn is clear, the strength of this preference divides scholars. While some claim that it is obvious from his inscriptions that he became almost henotheistic, others consider Nabonidus to have been similar to other Babylonian rulers, in that he respected the other cults and religions in his kingdom. His negative image could then be blamed on the Marduk priesthood, that resented Nabonidus' long absence from Babylon during his stay in Tayma, during which the important, Marduk-related New Year (Akītu-) Festival could not take place, and his emphasis on Sîn. In any case, there is no sign of the civil unrest during his reign that would have been indicative of trouble.