Answer : 2. "who"
Explanation :

• As we can see that this is a case of a relative pronoun we need to choose the pronoun wisely.

• As there is a verb just after the blank space we need to fill it with the subjective form.

• And for the person we use who and option 2 contains the pronoun ‘who’ and this will be the answer.

The correct sentence will be- The boy who came to see me this morning had come from Agra.