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为with复合结构，作saw them的宾语补足语。

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

划线部分为定语从句，修饰boy. 该定语从句为嵌入式定语从句，关系代词who在whispered的宾语从句中作主语。这种作主语的关系代词是可以省略的。