My father said let's all wait for the train together.
Literal
Father [topic-は] everyone [with-で] train [object-を] let's-wait [quotative-と] said.
The volitional 待とう ('let's wait') inside quotative と marks indirect speech reporting a suggestion. 皆で uses で to mean 'with everyone' or 'all together' — a common construction where で marks the group composition.