This is a great question. Napoleon is conspicuously missing in the battle of Cowshed. In chapter 4, where the battle takes place, he is mentioned only once. The text says that Napoleon and Snowball sent out pigeons to broadcast the story of the rebellion. After this, Napoleon falls into the recess. The one who takes charge is Snowball. In fact, Snowball is awarded a medal of honor for his role in the battle. The chapter ends with these words:
The animals decided unanimously to create a military decoration, ‘Animal Hero, First Class,’ which was conferred there and then on Snowball and Boxer.
This shows that the heroes of the battle and chapter were Snowball and Boxer.
All of this begs the question of where Napoleon was. The answer to this question is actually found in the previous chapter. There we see Napoleon's view. He did not believe in any of the committees that Snowball set up. He believed that he needed to start with the young. So, he took the pups of Jessie and Bluebell. Later in the book, these pups would become his muscle, that is, guard dogs.
Here is what the text says:
Napoleon took no interest in Snowball’s committees. He said that the education of the young was more important than anything that could be done for those who were already grown up. It happened that Jessie and Bluebell had both whelped soon after the hay harvest, giving birth between them to nine sturdy puppies.