、、。
As the investigation progressed, it became clear that the skull had been smashed by some heavy blow.
Literal
Investigation [object-を] advance [while-うちに], skull [subject-が], something heavy blow [object-を] receiving, is-shattered [nominalizer-の][subject-が] became-clear.
Narrative suspense prose. ~うちに attached to a verb in the non-past form means 'while X is happening,' 'in the course of X' — marking the temporal window during which the next event occurred. Inside the main clause, the nominalizer の turns the whole result-state clause (頭蓋骨が... 打ち砕かれている) into a noun phrase that serves as the subject of 明らかになる ('become clear'). 打ち砕かれている is the resultative passive of 打ち砕く ('to smash to pieces'), so 'is in a state of having been shattered.' Together these layers give the sentence its 'as we investigated further, it became clear that X was in this state' narrative shape.