In the sentence "The doctor phoned the nurse because he was late," the pronoun "he" most naturally refers to the doctor. So the doctor was late.

This interpretation follows the typical pattern where pronouns refer to the subject of the sentence (the doctor) rather than the object (the nurse). The doctor is calling to inform the nurse about his lateness.

However, it's worth noting that this sentence is ambiguous - without additional context, "he" could theoretically refer to either person, though the doctor is the more likely interpretation.
