The Evil Within is a very mysterious game that knows how to mess with your head. A lot of people could come up with an idea of what is going on in one chapter, but the next chapter will debunk that theory that you or others may have. There are many theories I have come up with that I feel can be supported.
WARNING: Spoiler Alert
Theory 1: The Boxman was really one of Ruvik's working partners
In Chapter 7 "The Keeper" in one of the tunnels to find the stones to open the way to Boxman there is a tape recording. The tape has Ruvik talking about a worker who stole his notes and talks about his harshly. This well placed tape helps one infer that Ruvik put the safe on that workers head to prevent him from revealing Ruvik's secrets.
Theory 2: Ruvik is in control of Leslie long before Leslie "dies"
In the final chapter the games starts to unfold to come to a conclusion. The conclusion I made is Ruvik is actually in control of Leslie sooner than we think. As Sebastian you follow Leslie for a good amount of time until you encounter Ruvik. There is a cutscene were Leslie stops and stands in the rain. The odd thing about this is Leslie starts to walk normal opposed to his normal shuffle. It gives him a sense of confidence that is unnatural for him.
Theory 3: Lily Castellanos's death was not an accident, but a murder
In the game there are journals, newspapers, and missing persons papers Sebastian can pick up. The first two reveal more about each character. They also talk about the events before, during, and after Lily's death in the house fire. Lily Castellanos was the daughter of Sebastian Castellanos and Myra Hanson, who are both detectives for the Krimson City Police Department or KCPD. They got a call that there house was on fire and that two bodies were discovered. One being Lily and an older Hispanic women who was her nanny. The journals reveal Myra investigates the fire only to disappear because of coming too close to the truth. It is reveal in the dlc that Myra was working for this group called Mobius and she believes they killed Lily because she was getting in the way of her "work."
Theory 4: The Spider Lady is actually Ruvik's sister Laura
In Chapter 4 you first encounter this bloody spider lady that you must run from. Then in Chapter 5 you must kill her with fire. In Chapter 9 you find out about Ruvik or Ruben's past and his sister died in a barn fire where he is badly burned around his body. You run from her once again in Chapter 10 where you cut her arms off in an elevator. Then it stops and Ruvik reveals how his in control of everything in a rapist kind of way. It does not directly state it, but it infers it with a tape recording the Chapter.