Models in or behind cover always fight first in close combat regardless of Initiative. This represents the advantage of cover – their attacks include not only close fighting but also shots against the enemy as they charge in. Apart from this cover does not affect hits or anything else in an assault. After the first round of close combat fighting is assumed to have swept into the cover so it gives no further advantage to models in it.
Troops who are defending cover have a massive advantage in an assault. They can fire from their hiding place at their approaching enemies and then smite them down as they struggle to get to grips with their hidden foe. It's all in the reflexes when it comes to combat in the open: slow lumbering opponents can be quickly dispatched by a faster and more agile foe. Unfortunately, lumbering opponents such as Orks are tough enough to be able to withstand a vicious pummelling and still come back for more.
In close combat models defending in or behind cover strike first. Resolve all their attacks and remove any casualties before moving on to the rest of the models. Fighting for the remainder is resolved according to the Initiative value of the models. Models with the highest Initiative attack first, then the next highest and so on.
Diagram: Who Strikes First. A Space Marine in cover strikes first. Dark Eldar strike first among the remaining combatants (higher Initiative, 5 vs 4).