Napoleon is not mentioned during the battle of the cowshed. It is unclear if he was involved in the fighting or if he was off to the side watching. Suffice to say, even if he was involved in the fighting, he did nothing significant. Napoleon is not mentioned during the battle for precisely this reason; he didn't do anything worth noting. Snowball and Boxer were the heroes of the battle. Subsequently, Napoleon and Squealer would spread propaganda that Snowball's actions were more traitorous than courageous. This had the effect of brainwashing the animals that Snowball acted cowardly and Napoleon, by default, was the only righteous leader they ever had.
Napoleon is strangely absent during the Battle of the Cowshed. We see no sign of him during the fighting. It is Snowball who charges bravely at the humans, accompanied by all 35 pigeons, all the sheep, Muriel, Benjamin and Boxer. At the end of the battle, Snowball and Boxer, who both fought bravely, are awarded the honor Animal hero, first class, but Napoleon is conspicuously missing from the honor roll. The conclusion one is led to draw is that Napoleon was carefully taking cover in the background while the other animals risked life and limb for the cause. We can assume Napoleon was there, somewhere, during the battle, because at the end of the battle Molly is noticed to be missing and everyone goes in alarm to search for her. Later, Napoleon will use propaganda to try to change the other animals' memories of what happened in this battle.