Halo 3 has a total of 13 skulls that can be collected spread across all missions of the campaign. You must be playing on Normal difficulty or higher in order for the skull to appear. Just pick up the skull in order for the achievement to unlock.
The skulls can be found as follows:
[
0:09] - Skull: Blind - Mission: Sierra 117
[
0:34] - Skull: Iron - Mission: Sierra 117
[
1:27] - Skull: Black Eye - Mission: Crow’s Nest
[
1:54] - Skull: Grunt Birthday Party - Mission: Crow’s Nest
[
2:33] - Skull: Tough Luck - Mission: Tsavo Highway
[
3:24] - Skull: Catch - Mission: The Storm
[
4:02] - Skull: Fog - Mission: - Floodgate
[
4:42] - Skull: Famine - Mission: The Ark
[
5:40] - Skull: Cowbell - Mission: The Ark (Grav Lift Required)
[
6:27] - Skull: Thunderstorm - Mission: The Covenant
[
7:19] - Skull: IWHBYD - Mission: The Covenant
[
8:38] - Skull: Tilt - Mission: Cortana
[
9:20] - Skull: Mythic - Mission: Halo
Collecting the above skulls will also unlock the following achievements: