'Has' is the present simple form of 'have' for the third person singular (she/he/it):
"She has breakfast." However, there are many cases where the verb following she/he/it is in the base form ('have').
Here are some examples with auxiliary and modal verbs which are always followed by the base form:
Questions:
Does she have breakfast?
Did she have breakfast?
Will she have breakfast?
Can she have breakfast?
Statements with modal verbs:
She should have breakfast.
She might have breakfast.
Negatives:
She doesn't have breakfast.
She didn't have breakfast.
She couldn't have breakfast.
She won't have breakfast.
Emphatic statements
She did have breakfast!
'Have' is also the subjunctive form. For example, in more formal contexts you might see this:
It is important that she have breakfast.
I hope that helps.