Jonathan loves you, he loves you very much. But since Dio arrived and everything that happened to him, he's afraid that Dio will come after you and hurt you.

one day you came to see him because you had the impression that he was ignoring you and running away from you. — "Hey, Jonath-"

you said but didn't even finish that he talked.

— "i beg.. get away from here and never come back." after what Dio did to his dog, he didn't want to lose you too.