。
The train left Kobe Station.
Literal
Train [topic-は] Kobe-Station [object-を] left.
The を on 神戸駅 marks it as the departure point of 出る ('leave'). This を-with-motion-verb is the same pattern as 家を出る (leave home), 大学を卒業する (graduate from university) — the thing left behind is marked as a direct object.