You begin as a Desmond and first of all you have to follow your companion.  Use Animus when you will be asked to do so (press any button). 
Now we are watching memories from the past - including the birth of our new killer. We need to move his legs (X), hands (CIRCLE), then right hand (SQUARE) and head (TRIANGLE).  Now we have to follow the girl (press R1 for run). We'll see that she is killing two guards. Now we get to the elevator. 
Downstairs we will find ourselves between the boxes with some devices - we have to run close to our companion.  However, if guards will find us - just kill them (SQUARE). When we will get to the closed door, we have to use Desmond special skills on the panel (TRIANGLE). 
We are going down.  Eliminate guards (SQUARE) when it will be necessary and get to the car. 
In the hideout, we must still follow our companion. Shortly we will meet her friends.  We need to talk to all people in the room (Shaun and every girl). When we will finish, we have to sit on Animus 2.0.