Chrono Triggertakes place in an Earth-like world, with eras such as theprehistoric age, in which primitive humans and dinosaurs share the earth; theMiddle Ages, replete with knights, monsters, and magic; and thepost-apocalyptic future, where destitute humans and sentient robots struggle to survive.
Homunculus is Eike Kusch's mysterious benefactor who is determined to help Eike prevent his death. However, this powerful being has a sinister purpose with Eike.
SPOILER WARNING: Plot and Ending details follow!
A complicated and Unknown History
The origin of Homunculus is unknown. It is unclear if there are others like him, how he came to exist and how he ended up sealed within thePhilosopher's Stone.
Because of the alternate timelines and his own time traveling abilities, Homunculus' story is difficult to understand. What is known is that, as the stone, he somehow came into the possession of Eike Kusch in 2001, before ending up in the possession of Dana when she was accidentally lost in 1580 by Eike. For the next four years, she kept the stone in her possession until she encountered Eike again, who had lost her a few hours before from his point of view. Homunculus was then returned to Eike, who went and gave it to an alchemist named Wolfgang Wagner.
Wolfgang Wagner freed the djinn form his prison, having dedicated his whole life to alchemy and the goal of creating the elixir of life and artificial life, was depressed and angry to discover that he only released Homunculus. At this point, history becomes complicated. When asked about it at a later date, Homunculus claimed that Wagner wished to be far away from Homunculus, allowing the djinn to make the alchemist vanish. Then, after the Wagner's Household had ended up destroyed few unknown means, the djinn met Eike before vanishing. However, in flashback it is revealed that Wagner wished to be young like Eike, who he was impressed by. Upon completing this wish, which revealed that Wagner was a younger version of Eike, Wagner then tried to seal Homunculus again. Despite succeeding by using a pentagram, Homunuclus cursed Eike with the "never ending night of eternal youth" which meant that Wagner was immortal and would suffer from reoccurring amnesia. As the Philosopher's Stone, he was taken by the memory-less Wolfgang Wagner.
Because of these two conflicting events, along with the large gap in time separating Homunculus from his first appearance (as the Philosopher's Stone) to the 1580s, it is unknown how Homunculus became free from the stone. However, it is possible that there are two alternate timelines that interact in 1584, which could explain how Homunculus became free. In one timeline, Eike kept the stone for centuries and forgot about it after being resurrected for the first time, and took it back to Wolfgang Wagner. Wolfgang Wagner then wished to be free from Homunculus, who then made him vanish and met Eike, not knowing who he was due to not meeting Wolfgang Wagner in his youth before. Then, Homunculus somehow made his past self appear near Eike so that he could take it back to 1584 to be given to Wolfgang Wagner, who then wishes to be young and reseals Homunculus, so the cycle begins again. This could mean that, through a complicated time loop, Homunculus created himself using his reality warping powers.
After being free however, Homunculus spent his time perfecting the plan to lead to his freedom by altering the timeline. At some point he swapped the infant daughters of the Wagner's and the Brums, thought was unable to successful replace the Brum's child with Margarete because of there being a large crowd. He also learned the existence of a powerful spirit in the former home of Wolfgang Wagner, which he stayed away from.
In 2001, he resurrected Eike from being killed by a time traveling Hugo Wagner, who had found his father's notes about Homunculus. Throughout Eike's adventure through time, Homunculus mainly resurrected him every time he died, thought at times he appeared physically to converse with Eike.
The End of the Story
Eventually, Eike returned the Philospher's Stone to Wolfgang Wagner as Homunculus had planned and learned that Hugo was the one trying to kill him upon returning to 2001. Hugo demanded that Eike find Homunculus, which leads to several alternate timelines, though most of them end the same way for Homunculus. With the exception of one, Homunculus would part ways with Eike, taking the digipad with him as he does. In one timeline however, he is accidentally injured by Eike, causing him to revert back into the stone and create a fully grown tree around him.
Losing Control
Unknown to Homunculus, after making Eike relive the events of his adventure so many times, the human had regained all his memories from all the timelines. As a result, Eike planned to escape Homunculus while in a new timeline. Grabbing hold of the Philosopher's Stone earlier than before, Eike came up with two plans to stop Homunculus.