Vaughan's mood swings aren't mood swings at all.
He actually has Multiple Personality Disorder due to the way the tumor is pushing itself on his brain. Charlie was pregnant at some point in the story.
Either Nate, Vaughan, or Harvey can be the father of the baby. Sissy and her family are all related to Nate through his mother's side.
Nate doesn't know this because his mom doesn't keep in touch with them, so he never met or even heard of them. Charlie has a mild case of Antisocial Personality Disorder.
That's why she acts the way she does while simultaneously having the ability to have real relationships with people. Dan survived being burned alive
Though he's most likely in a very weaken state and probably will be killed by zombies or something if he doesn't find someone to help him. Charlie loves Nate more than she does Vaughan.
She seems to care more about Nate than Vaughan as a whole. She doesn't just break up with Vaughan to be with Nate again because she too possessive over Vaughan and their break up made her too stubborn about dating Nate a second time. If Real Monsters became an actual part of the canon game, hardly anything would stay the same.
Executive Meddling is a bitch. Alternatively, alot would stay the same, but the alternative relationship between Nate, Vaughan, and Charlie would go.
Telltale Games is progressive, but they're not that progressive. One of the doctors is pregnant.
One of the things they took from Nate's truck was a bag of baby supplies. The reason why they didn't leave it with the food and whiskey is because someone needs those supplies. And the only reason why you'd need baby supplies is if you have or are expecting a baby. Vaughan never died.
Nate hallucinated his death. Vaughan is actually alive somewhere out there.