The IWHBYD Skull is located in The Covenant. To obtain the skull, start the level from the very beginning, and not from a Rally Point. When you reach the final scene, where the Prophet of Truth is planning on lighting the seven rings, proceed as you would normally: kill the Covenant, kill Truth, kill the Flood, but do not jump down the elevator shaft once you have finished that.
Once the bridge is devoid of enemies, you will have to jump through the seven holograms of the Halos in a specific order. When you have completed this, the IWHBYD Skull will appear at the beginning of the light bridge leading to Truth's podium. Note that you should not jump through the rings before Truth dies. Note you can work as a team in co-op (2-4 players) and work as a team to speed up the process. Just make sure you jump through the right rings, as it really speeds up things. Note: you can restart jumping through the rings without restarting the level over as long as you start from the beginning (eg: If you do 4.6.3 in accident, you can restart again)
The 7-ring sequence is as follows. Each number corresponds to the ring you must jump through; the ring at the elevator is 1, and the ring next to Truth is 7. The ring with red on it is 4. (Be aware that the order in which the rings are numbered for this sequence does not represent their actual installation number. In fact, the ring closest to the elevator is Installation 07.)
Sequence order: 4, 6, 5, 4, 5, 3, 4.
Once you have completed the sequence, the skull will appear at the beginning of the light bridge leading to Truth's podium. If you are not sure you got it, then look at the rings when you complete the sequence; they will be blinking in sequence. The Halo theme will play as you get the skull. You must then finish the level, or the skull will not be saved to your profile and you will have to get it again. You do not have to hold the skull until the end of the mission.
Each of the holographic rings sound a different tone of the E Dorian scale when you stand near it. The sequence, if you pay attention, plays part of the Halo theme song. Also, the rings in the citadel are holographic projections of the 7 Halo installations, the fourth being the newly reconstructed (and unfinished) Installation 04, the incomplete areas indicated by the red-glowing sections.
NOTE: If the Above Sequence of 4, 6, 5, 4, 5, 3, 4 does not work try, 1 3 4 6 7 5 4 6 5 4 5 3 4