Which one of the following sentences is grammatically correct and why?
- She baked а cake, but he had eaten it before you came.
- She had baked a cake, but he had eaten it before you came.
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The first one is confusing; it makes it sound as though the eating took place before the baking, which is not possible. The second one works fine, although it's a bit awkward to have all those past perfects.
There are two other possibilities that are smoother. The third possibility is to use past perfect to put the baking as far back as possible and leave the other two in past simple.
She had baked a cake, but he ate it before you came.
The fourth is just to rely on implicit ordering and leave all of them in past simple together.
She baked a cake, but he ate it before you came.
Because this last option is the simplest, and because in this case the order of events is clear enough without any special effort, it's the best choice here. However, only the first option is actually wrong, and sometimes the order of events is not clear enough without perfects, so keep the others in mind for other situations.