Well we do have a few options, some more likely than others. The Forerunners may seem likely at first, but when you really review the information we have, they fall apart. Yes they did fight a war with humanity over 100,000 years ago, approximately 10,000 years before the Forerunners fight the Flood. Yet consider this, the United States fought Germany twice, does that make Germany the US’ enemy? No.
Furthermore, the Didact, the Forerunners’ military leader, deeply regretted what he had to do when the war ended and felt pity at what humanity had before in the years after. That was the old Didact, the new Didact, aka Bornsteller Makes Eternal Lasting, actually has two close human acquaintances, Chakas and Riser, and expressed joy at finding them alive aboard Installation 07. Not to mention the wife of the Didact, the Librarian, deeply loves humanity as a race and did everything she could to preserve them.
The result? Well, humans aren’t constantly called “Reclaimers” for nothing. You could argue it’s a rouge Forerunner group, but why attack humans now? Why not the 100,000+ years humans evolved? Such a scenario would be forced and pretty stupid if you’ll pardon my French.
Now the Precursors, THEY do present a tangible threat. After all, it was the Timeless One, aka the Primordial, that said humanity would be tested by the Flood after it had matured. Fact is, the Flood the UNSC faced is nothing compared to what the Precursors have in mind.
So really, the Precursors have threatened humanity, the Forerunners…not so much.