He saw them with their heads together later that afternoon in the library, together with a weedy-looking boy Hermione whispered was called Theodore Nott.

with their heads together為with復合結構，作saw them的賓語補足語。

togetherwith a weedy-looking boy Hermione whispered was called Theodore Nott

劃線部分為定語從句，修飾boy. 該定語從句為嵌入式定語從句，關系代詞who在whispered的賓語從句中作主語。這種作主語的關系代詞是可以省略的。