since ... had

It sounds pretty damned awkward to me. I would have been more likely to have written:

In the first three months after 9/11, the US had captured 90 percent of the terrorists on US soil.

Whether or not one were to use an anterior past tense (had captured) would depend on the context, which you have not provided. I suspect that that sentence was not written by a native speaker of English. That misuse of "since" has the sound of someone translating directly from their own native language into English.

In the first three months SINCE 9/11, the US HAD captured 90 percent of the terrorists on US soil.

I think they meant:

In the first three months after 9/11, the US had captured 90 percent of the terrorists on US soil.

or


Within the first three months of 9/11, . . . . .

Round about December 11th, 2001, one could have written:

In the three months since 9/11, the US have captured 90 percent of the terrorists on their soil.

Later, one could write:

In the three months after 9/11, the US captured 90 percent of the terrorists on their soil.

Although how such a figure could be relied upon is beyond me. The terrorist in the White House is still there, I note.