Story related - can't be missed.
*** Spoiler - click to reveal ***
Happens in present day after Sequence 10 finishes (achievement "grim expectations")
You do this mission as Desmond so don't have the animus HUD but it's pretty much linear...
After the drive in the van you will arrive at the Abstergo offices.
Walk forward until stopped by guards....fight your way through and enter the lift.
Climb up the lift shaft.
Once out fight your way through and into the atrium area...you go through a window into the next area.
Then through a door for a cut scene with Cross
Follow Cross down the corridor and then through the broken window.
Chase him in the next room and assassinate.
Go down the corridor, fighting off the guards until you are allowed into Vidic's office.
Scenes...walk out with the apple...achievement