Transformation of sentence

'Had' is not needed.

The rain stopped (Simple past)
The rain had stopped (Pat Perfect Tense= sometimes, it needs two actions to say that it is in this tense)
The second sentence means that there are two actions in the past. The first action had finished before the second action happened.
For example, The criminal had stolen the money when the police came. (this means that the criminal had gone and had stolen the money before the police came. He had not caught. =]