As you gain control over Desmond, go to the upper floor and approach the gates.
Unfortunately the guards there won't let you pass.
In order to get pass them, start off by heading out through the door on the right.
That way you will reach a small courtyard with more guards.
Hide in the bushes and afterwards use the passage on the left.
Afterwards you will have to head forward, sticking to groups of people at all times. That way you will stay invisible to the guards.
As you reach the end of the room, go down the stairs to the toilet and exit through the other side.
A bit further you will find another passage, this time on the right.
Move onwards to an open window leading to a staircase.
The next floor is patrolled by an Abstergo guard. Follow him slowly and wait for him to turn around while hidden amongst other people. As he passes by, you will be able to move onwards to one of the boxes.
After you get there, climb the construction part and head to the opposite corner of the building.
Inside the corridor you will witness a murder.
Chase the murderer and beat him as he stops.
After obtaining the power source, the guards will start chasing you. Run away from him towards the underground. The path will be marked by blue markings. The mission will end as you enter the car.
You can now enter the Animus or use the obtained artifact. In the latter case, head to the previously opened passage to right of the machine.
As you listen to the goddess, keep running upwards while jumping between broken staircases.
As the stairs end, keep going onwards to the stone ramp. Don't climb it however. Instead, go down the stairs to the very bottom and enter the room on the left.
There you will be able to climb up the wall, to the next panel. Use it to unlock the next gate.
You should go there after collecting the third source. However for now return to the Animus.