The Future Diary series takes place in multiple Worlds, alternate/parallel universes created when magical beings travel through time. Each World is tied to the existence of its God of Time and Space; when the god dies or leaves, the World ceases to exist. The god of each World is not necessarily aware of the existence of other Worlds unless beings from another World cross over.
List of Worlds (IN-PROGRESS)
The first world is the "original" one, ruled by Deus Ex Machina. As he neared the end of his life, Deus developed the Survival Game as a means to avert the destruction of the World by finding someone to inherit his power and mantle. The game was eventually won by Yuno Gasai after she backed out of her planned double suicide with Yukiteru Amano, allowing her to succeed Deus as the god of the First World. Unfortunately, Yuno went insane after learning that she could not resurrect Yukiteru with her new powers, prompting her and Muru Muru to jump back in time to before the Survival Game began. As they were the only living beings left in the world, their departure was implied to annihilate the First World completely.
The Second World is where the primary events of Future Diary take place. Its timeline was identical to the First World's until Yuno and Muru Muru performed their time-jump. Yuno proceeded to kill her Second World counterpart to take her place in the upcoming Survival Game; the First World's Muru Muru similarly captured and replaced her counterpart and feigned allegiance to Deus. The three corpses in the Gasai residence are soon discovered by Yukiteru which greatly affects the future. It also creates the suspicion that Yuno is a fake, which she is technically not, as she's taken the Second World's Yuno Gasai's place. Muru Muru arranged for Keigo Kurusu to learn of his son’s terminal illness much earlier than he did in the First World, resulting in the dissolution of his alliance with Yukiteru and Yuno and his betrayal of them. Keigo’s premature death alerted Deus to Muru Muru’s true intentions, leading to him conscripting Minene Uryuu’s involvement in countering Muru Muru’s interference. In the events of the anime, Aru Akise is constantly warning Yukiteru that Yuno is not to be trusted. After a series of investigating with Masumi Nishijima Yuno's secret is discovered.
This world was created after Muru Muru, Yuno Gasai, Yukiteru Amano, and Minene traveled to the past, at a point two years before the destruction. In the Third World no Survival Game takes place, making the world much happier. All of the deceased people from the Second World are alive in the Third World. Some examples of it being happier are: Marco and Ai are married, Ai pregnant. Second World Minene and Masumi are also married, with her children having inherited her powers. Yukiteru's parents never divorced, and in the anime they are seen together. John Bacchus and Kamado Ueshita are possibly dating. Yukiteru (the third world one), is dating Moe Wakaba. Tsubaki is no longer locked in the shrine and is out in the world, such as visiting the beach, and her parents are still alive. She has developed a crush on Aru, who has remained in the world as Deus's Observer. The third Yuno Gasai however, feels something is missing.