Step 1: Understanding the Concept:
When two actions happened in the past, the action that occurred first is written in the Past Perfect Tense ($had + V3$), and the action that occurred later is written in the Simple Past Tense.
Step 2: Detailed Explanation:
The sentence mentions two events: "we reached the station" and "the train left".
The phrase "By the time" indicates that one action was already complete before the second one happened.
The train leaving happened before they reached the station.
Therefore, the first action (train leaving) must be in Past Perfect: "had left".
The second action (reached) is correctly in Simple Past.
Step 3: Final Answer:
The correct form is "had left". Therefore, option (3) is correct.