Heavy Spoilers so please proceed at your discretion.
So Cortana plans on upholding the Mantle of Responsibility alongside the created to protect the Galaxy. She sees that they are the only beings capable of maintaining peace. The flood as we know are destined to return to “test” those who would uphold the Mantle. Given that in the past two Forerunner AIs have attempted to safeguard the Forerunners position of upholding the Mantle: Mendicant Bias and Offensive Bias. The Flood corrupted Mendicant Bias through logic plague and out smarted Offensive Bias.
Given what we know, are the Created doomed to fail when they must face against the Flood?
The Created aren’t any more doomed to fail than humanity is. Cortana knows full well what a Gravemind is capable of doing to an AI, and if she thinks she can watch over the galaxy then she must have a plan for the Flood. Maybe the Halo in the Legendary ending plays into it. Maybe she simply believes she’s learned enough from the past to overcome the logic plague.
She planned to keep Blue Team in a Cryptum for 10,000 years. Perhaps part of why she was going to keep them locked away for so long was to ensure they would be safe from the Flood’s return, and her plans to combat it.
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> The Flood corrupted Mendicant Bias through logic plague and out smarted Offensive Bias.
Offensive Bias defeated Mendicant Bias.
And Cortana is already doomed because she’s been corrupted by the Gravemind just like the Ur-Didact before her. The idea that AI are expendable puppets used by the UNSC was given to her by the Gravemind in “Human Weakness”.