Ya habíamos embarcado cuando empezó la lluvia.

Questions & Answers about Ya habíamos embarcado cuando empezó la lluvia.

Why do we use habíamos embarcado instead of the normal past tense here?
This is the Pluscuamperfecto (past perfect), which acts as the past of the past. Because you finished boarding before the rain started, you need habíamos embarcado (we had boarded) to show it was completed first. The later event uses the simple past: empezó (started).
Could I put ya between habíamos and embarcado, similar to how we split verbs in English?
No, in Spanish you can never put a word between the helping verb (habíamos) and the past participle (embarcado). Adverbs like ya (already) must go before or after the entire compound verb, and placing it right before is the most natural choice here.
Why is empezó in the preterite tense rather than the imperfect?
The preterite empezó is used here because the rain starting is a sudden, specific event that happened at a clear moment in time. If you used the imperfect (empezaba), it would sound like the rain was gradually starting over an undefined period, which does not fit the sudden interruption happening here.
Since embarcar looks like it contains the word for boat, does it only apply to boats?
No, while it originally comes from boarding a boat or ship (un barco), embarcar is the standard Spanish word for boarding an airplane or a train as well.

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