However, the shape of Santorini has changed several times throughout history. The original island of Thera was circular, with the volcanic cone of Strongyli (translated as "one wheel") rising in the centre. The volcano grew over its long history and showed its true strength after alternating periods of calm and moderate activity. Around 1600 BC, an explosion so massive that it literally blew the entire volcanic crater apart, creating a caldera in the centre of Santorini that was immediately flooded by the surrounding sea. In 236 BC, Thirasia was separated from the rest of the island and, thanks to volcanic activity, two new small islands subsequently appeared in the caldera. Today, the archipelago of Santorini consists of the largest island Thera (which looks like a horseshoe surrounding a small bay, according to others like a gaping jaw), opposite it the smaller island Therasia and the tiny island Aspronisi, and in the middle of the caldera two small islands Nea Kameni and Palea Kameni.

Scientists from various disciplines are still trying to pinpoint the date of Strongyli's most massive eruption, and the latest they have arrived at is 1646 BC, when, after a series of smaller earthquakes and explosions, the accumulated energy was released in one of the largest explosions in the history of the entire planet. An incredible amount of lava, ash and volcanic gases spewed out of the crater. The caldera formed in the centre of the island quickly filled with water and a series of tsunamis followed, with devastating effects on the nearby and more distant surroundings of Santorini, especially the nearby island of Crete and the Asia Minor region.

According to archaeologists, this catastrophe was the cause of the end of the entire Minoan civilisation, which was very advanced and unique in its time. Thus, the event is sometimes referred to as the "Minoan eruption" because it destroyed both the Minoan city of Akrotiri on the island of Santorini and the Minoan palaces and the very advanced palace city of Knossos on neighbouring Crete. There is no evidence of a revival of Minoan culture on Santorini after this period.

The eruption of the Santorini volcano is also linked to the origin of the story of the so-called mythical Atlantis, a land where a highly intelligent civilisation lived, but whose end was caused by a great natural disaster. We learn about Atlantis from the writings of the Greek philosopher Plato, but exactly where this legendary land was located is still a mystery and a topic of speculation. One theory is that Atlantis could have been either the island of Thera itself, with its advanced Minoan civilisation, or one of the nearby islands that was flooded by a devastating tsunami after the explosion.

The Minoan city of Akrotiri was buried beneath a thick layer of ash and pumice after the massive eruption, much like the Roman city of Pompeii, which suffered the same fate after the eruption of Vesuvius (hence the archaeological site of Akrotiri is sometimes referred to as "Greek Pompeii"). The Minoan settlement thus remained perfectly preserved until 1967, when the Greek archaeologist Professor Spyridon Marinatos began to systematically uncover the remains of the ancient city. Unlike Pompeii, however, neither human remains nor many jewels and valuables were found in Akrotiri, suggesting that the city's inhabitants had been warned of the volcanic eruption and most of them managed to escape. However, the frescoes could not be carried away and thanks to the protective layer of ash, we can now admire their magnificence and sophistication. Beautiful frescoes with natural themes, religious paintings, abstract works and scenes from the everyday life of the inhabitants have been preserved. Excavations are still taking place here today and the archaeological site of Akrotiri is one of the most valuable monuments on the Greek island of Santorini.

Santorini lies in a very seismically active area, where one tectonic plate underlies another. This includes the other volcanoes Methana, Milos and Nisyros. Santorini is a "dormant volcano" but still active. Its last major eruption so far occurred in 1956, killing many people and completely destroying several Santorinian towns. Since then, the volcano has leaked mainly gases, but underwater lava outpourings have also been recorded.