Like many prehistoric monuments, the Neolithic Temples of Malta have been the subject of astronomical studies, aimed at identifying possible alignments with cosmological events. The orientations of several sites have been suggested as evidence of an interest in the movement of the sun, moon, and stars, and of the importance of certain days such as the equinoxes and solstices. However, while individual sites may seem to align to specific events, a wider study into patterns of orientation is needed to determine whether these are the result of human action or random chance. In this paper, alignments at extant sites are investigated through 3D simulation, providing new data and statistical evidence for (and against) previously identified alignments. The methodology proposed uses Raycasting in Unity3D to identify the accuracy of orientations throughout the Maltese Neolithic (3700-2400 BC) at 23 temples sites. The orientation is analysed in relation to plausible astronomical events, as suggested by material evidence. The data produced shows possible patterns of alignment, rejecting commonly accepted targets such as the sun, in favour of a cautious acceptance of an alignment with the constellation of Crux. This shift in focus alters heliocentric interpretations of Maltese temple culture, while also supporting a wider landscape cosmology. This study demonstrates the use of 3D simulations as a tool for investigation of archaeological queries. The research not only provides a new methodology for the automatic calculation of alignment patterns, but also establishes how 3D simulation can create new data which can impact current archaeological theories.