An indirect command is a sentence such as "I ask/advice/command/persuade (etc) you to come'. In these instances, the infinitive in English becomes 'ut + subjunctive' in the Latin (or 'ne + subjunctive' if the infinitive is negative i.e. I ask you not to come). If the verb in the principal clause is in the present, future, future perfect or perfect (e.g. I have asked) tense then the sentence is in primary sequence and the verb in the subordinate clause will go into the present subjunctive. If the verb is in the imperfect, past (e.g. I asked) or pluperfect tense then the sentence is in the historic sequence and the verb in the subordinate clause will take the imperfect subjunctive.
Further help could be given on how to form the subjunctive if that was also a problem for the student.