The answer that correctly completes the sentence is "had run." This sentence is in the past tense and so only verbs in the past tense or past perfect tense can be used to complete the sentence. 'Had run' is in the past perfect tense which indicates an action that already has happened.
In the case of run, the verb is in the present tense.
In option C, have run, the verb used is in the present participle tense.
Option D, is wrong because there is no verb as runned in the English language. Past tense for run is ran.
