Humans never destroyed the Forerunners. The Forerunners were the ones that devastated humanity. War between them started after automated ships were found to contain viles of a powdery substance. It was examined by Humans and Prophets and there was no harmful effects found with it. In fact, it was used as a breeding mechanism of a popular species of pets. But eventually the genome of these pets greatly mutated and created flood forms. Because many people were keeping these things as pets, the infection spread quickly among human populations. Now you have this infection spreading to Forerunner worlds and the Humans were trying to stop it so they attacked these worlds. Humans tried to explain to the Forerunners that the Flood was the reason but they thought it was a made up story and war ensured. Facing a two-front war, humanity eventually lost. Once Humans were defeated, the Flood left the galaxy. Now the thing is that Human scientists found a cure but when the Forerunners devolved Humans, this knowledge was lost. Years (like centuries or millennium later) the Flood returned to the galaxy on non-military commercial ships. They were able to get past Forerunner defensive and crash landed on the surface of planets which caused the populations to be infected, creating millions if not billions of new Flood forms. The Forerunners were all about the Mantle and protecting life so conducting wide-spread bombardments on planets was not an option. Well eventually it did become an option but it was already too late as Forerunners had gone multiple plans before hand which none worked. They eventually realized that the only way to stop the Flood and protect all life in the galaxy was to build the Halo Arrays to wipe out all life, voiding the Flood of it's food source, but keep samples of each species "on file" so worlds can be repopulated again. This meant that the Forerunners would become extinct. Now there is a prophecy saying the Flood would return to galaxy and it has yet to happened. You may thinking "what about Halos 1-3". Well good thinking because that technically isn't the prophecy. What had happened was the Forerunners kept some Flood isolated on the Halo installations and during the events of Halo:CE, the Flood was accidentally released. What the prophecy is talking about is the Flood coming coming from beyond the reaches of the universe in the numbers like the Forerunners experienced