Dr. Stone is a manga-anime originally written by Riicho Inagaki and Boichi. It centers around Senku Ishigami, a high school science genius who spends most of his time in the laboratory working on different science experiments and projects.
One peaceful day, Taiju, Senku’s friend, decided he was going to end his long-time unrequited love and confess to the girl he likes. However, just as he begins his confession, a bright green light was seen on the horizon, and everyone suddenly turned to stone.
Senku wakes up billions of years later to find that the earth is now back to its original state before civilization began. Buildings are covered with trees, vines, and everything from the world he knew in high school is now buried underground.
However, this did not kill Senku’s spirit, instead, he and his science-filled, genius brain worked on different formulas and experiments to undo the petrification. When he finally had the perfect formula, he revived his friend, Taiju, and they began rebuilding the world.
Now back to the question, why exactly did the petrification happen?

The last arc of the Dr. Stone manga is currently ongoing. However, the person behind the petrification was already revealed. The villain of the story is Why-man. But, the ones who started the petrification were a bunch of Medusas who wanted to test if humans wanted death or immortality.
Honestly, we should have seen that one coming. The petrification was meant to be an experiment on the human race. This is because, as explained by the Medusas, humans are one of the species that have the high intellectual capacity to recognize that petrification could keep them alive forever.
Apparently, the petrification breaks easier with high mental activity. If you can recall, Senku counted every second he was petrified so he could keep track of the date. This mental activity was the reason he was the one revived first.
More on the petrification and Senku’s decision will be seen in the next chapters of the manga.