The Amalgamation

The Amalgamation was a theoretical event in which the Seed and all of its Amalgamates would successfully assimilate all organic matter in the galaxy. There were two instances in which the event almost reached completion, but fortunately it was prevented both times.

The First Infestation
During the Architects' misuse of the Codex, they unwittingly created the Seed. Once it achieved sentience, it escaped from its containment within the Codex itself, and proceeded to consume all available organic matter. Though it seems that the Architects were its primary target, Al'cor mentions other species falling victim to it as well.

On the brink of extinction, the Architects devised a method of staving off the event until a later date; not quite stopping the Amalgamation, but halting it for the time being. They used the fold-weapons to transport the Seed within the core of the world of storms, and sealed their collective consciousness away inside the Codex. When Tobias Four sent the Seed forward in time, the crisis was considered averted.

The Return
Millions of years passed for the galaxy before the Seed and the Amalgamates resurfaced, though only moments had passed for them. It immediately set about continuing with its original plan, spreading throughout the frontier and converting human colonies into more Amalgamates. It is unknown if the core worlds were affected.

Ultimately, the Amalgamation was brought to an end by the efforts of Tobias and KT-0298 who assisted in Harmony's Last Stand. By activating the Tempest arrays, the Seed's extra-dimensional consciousness was torn apart, effectively severing its connection between itself and the Amalgamates and resulting in its death.