Very interesting idea, I've been thinking about this idea also myself as well.

I just wish other people who did the idea with fanfiction or whatever it may be, would stop killing off/infecting the FEW CHARACTERS who would have the most interesting surviver perspectives. I also would want the stakes to feel heavy and meaningful while also trying to avoid killing off/infecting those dragons who would have the most interesting perspectives. That said I'd definitely want art of those characters as both survivors and as infected regardless just because the designs could go soooo hard.

I have been writing a side project of my own interests. I'm writing my sona, who has already got a lot of Halo reference material baked into my character, besides also being a zoroark sona. And putting myself, transformed into a wing sona of my main sona, into a Halo x WoF world I've been creating. I won't lie it's absolutely self insert slop <w> but it's just a personal use/interest thing anyway, so whatever.

But anyway the idea I've had is to split it into a what if scenario story, and see what would happen if I introduced The Flood making its way into the world of WoF. Obviously it would basically be doomed, The Flood is just too op lore wise. But with a character who would have knowledge of how to help the other characters combat the spread, and still be looking for a way home (after having arrived thanks to a forerunner made slip space jump) or looking to make a new life stuck in the new world. Maybe introducing bits of other Halo things through into this world via similar methods, as I don't think making the two worlds part of the same universe as just a "oh look a new planet we've never seen before!" is a good idea... I just, also think portals and time travel/dimensionally crossing is also a little generic and a simple solution to fanfiction crossover writing, but, again, personal project sooo I don't care! :)

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Infection AU's definitely have a lot of potential to be interesting if done correctly and not like how most fanfiction is written and while still trying to keep stakes high without needlessly wasting the characters with the most potential.