Halo: Silentium: Book Three of the Forerunner Trilogy by Greg Bear
In the last years of the Forerunner empire, chaos rules. The Flood - a horrifying shape-changing parasite - has arrived in force, aided by unexpected allies. Internal strife within the ecumene has desperately weakened Forerunner defences.
Too little, too late, the legal rate of Juridicals is only now investigating possible crimes by the Master Builder and others. Evidence-gathering agents, known collectively as Catalog, have been dispatched to collect testimony from the Librarian and both Didacts: the Ur-Didact, treacherously abandoned in a Flood-infested system, and the Bornstellar Didact, who accompanies the Librarian as she preserves specimens against the dire possibility of Halo extermination.
Facing the imminent collapse of their civilization, the Librarian and Ur-Didact reveal what they know about the relationship between the long-vanished Precursors and the Flood. The Precursors created many technological species, including humanity and the Forerunners. But the roots of the Flood may be found in an act of enormous barbarity, carried out beyond our galaxy ten million years before.
Because of that barbarism, a greater evil looms. Only the Ur-Didact and the Librarian - husband and wife pushed into desperate conflict - hold the keys to a solution. Facing the consequences of a mythic tragedy, one of them must now commit the greatest atrocity of all time - to prevent an insane evil from dominating the entire universe.