Near the start, kill the clone soldier that is by himself. Then, look at one of the security cameras.
Before the first apparition of Charles' face, check the broken down door right over the table. Look into it to hear Alma crying. However you normally cannot see her.To actually see Alma, go back to the pair of double doors you saw before you saw the broken table. Keep opening and closing them. After awhile, the "Incoming: Unknown Origin" will appear. Keep doing this. After a few more minutes, the doors will disappear and you will enter a paranormal vision.
One of the people communicating to Betters and the SOF-D team is named "A. Sheppard". This is a reference to the main character of Half-Life 2: Adrain Sheppard.
When Alma takes you into the vision, turn around after the door explodes or else you will take damage from a nightmare.
To the scene skip when Alma appears on the ladder, simply jump down instead of climbing down. This however will use up some life and therefore is not recommended.
After you defeat the group of men and a cyborg wielding a Penetrator in a large room, go through the doors and onto a balcony with plants underneath. Use the ASP rifle to kill the two men that are attacking from below. Do not jump down to where they were. There is an very large cyborg with a multi-rocket launcher waiting for you. Instead, jump directly across from the doors you just came through. Hide behind the first obstacle you find. Get out from your spot and shoot the machine with your ASP once to draw its attention so that it comes towards you. Once you get its attention, quickly get back to your hiding spot. When you hear it has stopped walking, lean out from your spot. It will not notice you, even after you start attacking. Keep shooting it until it explodes.
To skip the scene with Fettel kidnapping Alice (even though it is an apparition), simply shoot Alice or Fettel. You will however find an additional scene with Alice's body on the floor (also an apparition). This might be a sign of the future though because Alice's body is discovered in Interval 10 in the same way.
In the last interval, beware when Alma attempts to go after you in the last vision. On Hard mode and above the rooms will be pitch black, allowing Alma to hide and attack you without being seen. Pay close attention to anything that appears to be moving in this last vision. Also, the flashlight and slow motion will be useless.