I came there.  They had left.

-->When I came there, they had left

-->Before I came there, they had left

-->After they had left, I came there

-->  By the time I came here, they had left

2. John went home. He had gone to the store.

-->When John went home, he had gone to the store

-->Before John went home, he had gone to the store

-->After John had gone to the store, he went home

--> By the time John went home, he had gone to the store

3. The train had left. We arrived at the station.

-->When we arrived at the station, the train had left

-->Before we arrived at the station, the train had left

-->After the train had left, we arrived at the station

-->  By the time we arrived at the station, the train had left

4. They went home.They had eaten a big roasted chicken.

-->When they went home, they had eaten a big roasted chicken.

-->Before they went home, they had eaten a big roasted chicken.

-->After they had eaten a big roasted chicken, they went home

--> By the time they went home, they had eaten a big roasted chicken.

5.He had cleaned the house by the time her mother came back.
-->When her mother came back, he had cleaned the house

-->Before her mother came back, he had cleaned the house

-->After he had cleaned the house, her mother came back

--> By the time her mother came back, he had cleaned the house