Aside from having the same type of ridiculous city names, there are quite a few references here and there, and Sebastian doesn't seem too surprised when he encounters the Haunted for the first time. Perhaps he is already familiar with T-Virus zombies and B.O.W.s?
Let's just do the math here: we have one supposedly-dead character (Laura Victoriano) who we know survived, albeit in a coma; and one mysterious main character (Juli Kidman) whose past is unknown and who's constantly referred to as "kid". Though I can understand the theories where she's thought to be Sebastian's daughter, I prefer to believe she's Laura.
- Jossed: In the DLC, it's revealed she remembers her past, and she's related to no other character but a Mobius agent.
There is a clue to this even before he sees Leslie walking away from the hospital. When Kidman is telling her colleagues to leave the deceased behind, she says "They aren't going anywhere; no one can." Paraphrased for lack of memory. That last line: no one can. What does that mean. I believe it means she knows they failed. Ruvic's plan has succeeded, and he is now out in the real world, while all of them are still trapped in the world he created. And now have no hope of ever leaving.
Ruvik logically would be confined to STEM, right? He can't -actually- run around and slice the throats of police officers left and right. Kidman's organisation are feeding people into STEM in an attempt to get rid of Ruvik from the STEM system, so that they can use it for something else... Joseph and Sebastian are fed into the system by Kidman, as her organisation may have believed that police officers would get the job done quicker than random civilians, thus why they sent her undercover to spy on them & put them into the STEM mind link. Sebastian is guided along pre-laid rails (the photographs in chapter 6 show that he has no real free will, along with the 'flash forwards' that he gets, such as of Joseph being dragged away by haunted in chapter 5 when the event happens in chapter 6) and he does end up destroying Ruvik. This event seems to be metaphorical, as there is no sign of damage to the case or any sign of a brain ever being there when Sebastian 'wakes up'. What ACTUALLY happened was that Sebastian handed over control of the STEM world to Kidman's organisation. (When Kidman talks to Sebastian in the bathtub, she states "[you're] not going anywhere... No one can.")
Essentially, Sebastian did not 'wake up'; he is now confined to the STEM world along with Joseph. Kidman and co. now have full control, rid of Ruvik. What do they plan to do with this mini world? I guess we'll find out in the DLC.
- Partly confirmed. The Assignment reveals Kidman has been sent into STEM to remove Ruvik from the system (at least, this is what they tell her.)
Ruvik is only a Reality Warper because he's in control of STEM. Escaping it (assuming he did) leaves him locked in a rather unhealthy-looking body that may or may not be suffering from chemical imbalances, on top of Ruvik's own brand of crazy, with zero resources to recreate a STEM system. At the same time, Ruvik rigged the STEM to only work if his brain is hooked up to it, so that's no longer functional. In the end Mobius is left with a useless machine they might be able to reverse-engineer in a few years. Compared to what would have happened if Ruvik was left trapped in STEM, potentially able to extend his field of influence?
- Additionally, Leslie is wearing what looks somewhat like a straightjacket, and people would undoubtedly find his file, leaving Ruvik/Rubin with the sticky situation of mimicking Leslie's condition. He also has no food or money, and if Leslie has friends/family on the outside, what happens if he runs into them?
Maybe Joseph's not actually in the STEM. The Joseph you meet in-game could be a mental projection set up by Sebastian. Sebastian could've assumed that his long-time partner is somewhere in here too, or wanted Joseph to be here to help, and subconsciously manipulated the system into manifesting a fake Joseph. Also, if this Joseph is just a mental projection, it could contribute to how easily Ruvik can manipulate and use Joseph to his advantage.
There's symbolism at the beginning of Chapter 1 which I'm almost 100% certain will be followed up on:
When the detectives come out of the car, Joseph and Sebastian share their character defining shot, with Kidman having hers in isolation. This shows that currently, Sebastian is aligned with 'Good', AKA Joseph, rather than 'Evil' which Kidman represents with her ambigious antagonist position. Essentially, Joseph is a metaphor for the concept of 'Good' and Julie for the concept of 'Evil'.
Immediately following their character shots, Joseph and Kidman walk in front of Sebastian and go seperate ways around the little front garden to reach the door of the asylum. The player is essentially given a small non-consequential choice on which character to follow. Kidman stays silent when you follow her, exemplifying the easiness of descending into mayhem and chaos, but perhaps the lack of community that arrises as a result.
Joseph does make commentary on his route - he states to Sebastian something along the lines of "They left their weapons in their cars" - and his route has an ambulance on it. The ambulance represents the bumps that can occur along the way in attempting to remain lawful, (which is reflected in poor Joseph's treatment throughout the game - being on the edge of turning, chased, sniped, nearly beheaded, etc. The same ambulance is even seen in chapter 12, which Sebastian is running to to get supplies for a dying Joseph!) but "leaving their weapons in the cars" = a promise of peace at the end of the road, and companionship.
A 'choice' between good and evil is not a very big part of The Evil Within, but as the game begins to develop into a franchise, this choice and the philosophy behind it seems as if it will be a significant theme of the series.
Sebastian is the protagonist of the main game; Kidman is the deuteragonist, and the protag of two of the DLC packs. Joseph has very purposefully been left out of the limelight; he is last seen in chapter 13 after having been shot by Kidman, unlike Sebastian and Kidman herself who both appear to have made it out of STEM untouched.
The implications are that Joseph is still alive, but he has been 'moved' by Mobius; this appears to have been done because he managed to figure out how STEM worked. (Notice Kidman's expression and interest in listening to Joseph explain the situation to Sebastian.)
Leslie was a very important part in making Ruvik stronger & it is again heavily implied Ruvik escaped in Leslie's body; Joseph's conspicuous dissapearance seems to suggest that he will be the key to remedy this problem, or some sort of problem, and this is the reason why he is not explored as much as his two partners.
It's hinted in the game several times that Leslie has a certain level of influence in Ruvik's dream world, and he was the only one to survive previous experiments linking others' consciousness to Ruvik's. Perhaps Leslie created the safe room during his previous visit, which allowed him to escape. In addition, Leslie can be found in the safe room multiple times, and its dilapidated state later in the game may symbolize Ruvik worming his way further and further into Leslie's psyche.
Come on, everything about him is screaming that he is Slenderman. The suit, the tentacle shadows, the video distortion when he is approaching.
As soon as he gets into the ambulance, he's already unconscious and the rest of the game is him in a hospital living through a nightmare fever dream while the doctors try and pump him full of enough antibiotics to make him a walking pharmacy. Joseph, it turns out, is being hailed as a hero on television as he leads the investigation after alerting Dispatch they need either all their HRT officers or the National Guard.
- Confirmed in The Consequence. That she works for Mobius anyway. As to her reasons we can only guess though it is most likely about Lily.