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The final Halo Infinite Season 4 Infection intel just released and it looks like the Season 5 Flood content is going to be canon. As explained by Reddit user MilkMan0096, this is the first indication in Halo canon that a Spartan has been infected by the Flood. CORRUPTER and UPSILON are Flood containment protocols, with CORRUPTER specifically being the authorization of use of weapons of mass destruction to annihilate Flood Infected Spartans.

Basically the first ever time Flood infected Spartans has been canonised in Halo!