2. We do not know what he is doing.
3. I do not know how many ships there were.
1. Dic mihi cur timeas (verearis, metuas).
2. Nescimus quid faciat.
3. Nescio quot naves (quantum navium) fuerint.
Feel free to discuss, correct, explain, and argue in a scholarly manner
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Synopsis of material:
A Subordinate Clause is a Clause (i.e. a pocket of a sentence, or sentence itself which contains a complete or semi-complete thought with a verb) that fits into a main sentence, such as an Indirect Question.
Ia. The sequence of tenses is that with Primary Tenses (Pres. or Fut., sometimes Perf.), and Imperatives, a subordinate clause At the same time or After the main verb is referred to in a Present Subjunctive in the Subordinate Clause. So, if the Main Clause's verb is in a Primary Tense, such as that of Present or Imperative, as in sentence 1 or 2 above, the Subordinate Clause's verb must be in the present subjunctive if we wish to speak at the same time, which we do:
Thus, in #2, nescimus is a translation of the present verb "we do not know". "What he is doing" is to be translated in the present (facit), and since the rule is that a subordinate clause in the present with a main clause in the present becomes a present subjunctive, it becomes faciat.
Ib. If we wish to express time before a Primary Tense Verb, we use the Perfect Subjunctive as in sentence 3 above.
Thus, nescio is a translation of a present verb "I do not know". "How many ships there were" is to be translated in the past (erant or fuerant), and since the rule for past verbs in subordinate clauses with present main clauses is that they are put into the perfect subjunctive, it becomes fuerint.
IIa. The sequence of tenses is that with Historical Tenses (Imperf. or Plup. or Perf.), a subordinate clause At the same time or After the main verb is referred to in an Imperfect Subjunctive in the Subordinate Clause. So, if the Main Clause's verb is in a Historic Tense, such as Pluperfect, the Subordinate clause's verb must be in the Imperfect subjunctive if we wish to speak at the same time. Let's use the example "He had asked what she would wish":
We could translate "He had asked" as rogaverat, a pluperfect verb in the main clause. Then "what she would wish" is a speaking of the future (volet), and since subordinate future clauses with past main clauses are put in the Imperfect subjunctive, it becomes vellet. Thus we should have Rogaverat quid vellet.
IIb. If we wish to express time before a Historic Tense, we use the pluperfect subjunctive. I'll use this sentence... "I know (cognovi) what you had considered":
While cognovit is often translated in the present, it is technically a past tense verb in the perfect, putting the main clause in Historic tense. Therefore, we shall translate "I know" as cognovit. Then "what you had considered" is speaking of the past in relation to the main clause (cogitaveras), but since subordinate past clauses with past main clauses are to be put into the pluperfect subjunctive, we have cogitavisses. So it would read Cognovi quid cogitavisses.

