[8] During the excavations, a portion of the contents of the Hypogeum, including grave goods and human remains, were emptied out and discarded without being properly catalogued.

[9] Zammit began publishing a series of reports in 1910 and continued excavating until 1911, depositing his findings at the National Museum of Archaeology in Valletta.

[13] Later archeological excavations indicate there was once a surface shrine that marked the entrance to the Hypogeum, with its subsequent destruction likely shielding the lower structure from discovery for thousands of years.

[13] The underground structure may have originated from a natural cave, expanded over time by cutting directly into the rock with crude tools including antlers, flint, chert and obsidian.

The temple structure uses a careful direction of light from the surface to penetrate into the lower chambers, with intricate patterns painted on portions of the ceiling with red ochre, following motifs of spots, spirals and honeycombs.

[18] A resonance niche cut in the middle chamber, called the Oracle Room, was possibly designed to project chanting or drumming throughout the rest of the Hypogeum.

[1][19][20] A broad range of objects were recovered from the site, including intricately decorated pottery vessels, stone and clay beads, shell buttons, amulets, axe-heads, and carved figures depicting humans and animals.

The figures range from abstract to realistic in style, with major themes thought to be related to veneration of the dead and spiritual transformation.

[21][22] The Hypogeum is constructed entirely underground and consists of three superimposed levels hewn into soft globigerina limestone, with its halls and chambers interconnected through a labyrinthine series of steps, lintels and doorways.

The renovated museum was inaugurated by Minister for Culture on 28 April 2017 and includes a new climate control system for the Hypogeum as well as an expanded visitor centre.