The Eden of Grisaia: Bad Ending

At the end of Yuuji's battle with Heath Oslo, he is introduced to the "First" Heath who is in a wheelchair and living on machines. This is where he finds out that the name Heath Oslo is actually a title given to the one that takes over their organization. The man that he killed was the second Heath Oslo a cloned copy of the first. But the first is soon to depart from the world and he makes a request to Yuuji. "Become the next Heath Oslo, make the world the way you want it by making mankind your enemy." The Organization that Heath Oslo runs is based on ensuring that wars are fought and then subdued and they profit from these wars. When one nation gets too strong they find ways to bring them back down, when a nation is on the brink of destruction they go in and raise them back up from the ashes. They create the 'balance' of the world.

If you choose to accept this offer you become the new Heath Oslo and you have your sister join you in the organization. There is a very short scene that has Yuuji and his sister talking about what is to come as well as the girls that he left behind. The girls are on the island that he was given creating a new life for themselves and waiting on Yuuji, though he will never get a chance to see them again. He has made the decision that he will not see them, or more so they will not see what he has become.

Effectively with his sister at his side he has gained all of the Thanatos System and now holds a very powerful trump card against the largest and most powerful nations of the world. His sister can enter the system at will using a pod to connect to the system. When he makes the remark about why she joined him her only response was she gave, in essence, was "my brother is the most important person in the world, and my love for him is endless. If he wishes to change the world by becoming mankind's enemy I will do the same." 

In a way, I don't really know if this would be a "Bad Ending" per se but it is certainly one that is different. Plus from what is said and stated I think it goes without saying that the siblings have more than just a...family relationship. Though this has been pretty much verified through the entire thing.