Like its name suggests, the combined world is the mystical fusion of the modern world (the protagonist's home) and the parallel world (alternate end of the Tokugawa shogunate). According to the deity of time, it is a world that will be created in the distant future. Yet his ambitions, the disturbance of the Five Elements, the summoning of the Four Fiends, and Zhulong's consumption of the worlds' energies has quickened its emergence. The new merge starts in December 2020 in the modern world, January 1866 in the parallel world.
When the combined world is born, the modern world and the parallel world are obliterated for its completion. Since the protagonist never sees the world herself, it's difficult to determine how much of each world remains. The landscape is a giant desert; flora or fauna are scarce, yet humanity in the future is somehow able to survive. The members of the Star Clan, at least, are able to prosper. Their legends of the parallel world and their powers of foresight still exist.
During the games' story, the modern world is the first to see symptoms of the fusion. People and plants have vanished, and the cityscape of Tokyo is in ruins. The surrounding terrain has already become barren. Only a few buildings are intact. To restore the flow of the Five Elements of her home, the protagonist gradually uses her priestess powers to resurrect certain landmarks.
In Harukanaru Toki no Naka de 5, the protagonist's main goal in the majority of the timelines is to prevent the combined world's birth. Once she learns the truth of the Kiryu siblings, however, she wants to protect all three worlds to avoid ruining the natural future.