I have an idea of how 343i can write Halo 6 in such a way that if might just save the franchise.
First, they need to release a prologue to Halo 6, much like Kojima did with Ground Zeroes. This will establish both the mechanics and plot, for the game.
The following is the plot of the prologue to Halo 6:
You play as a flood spore. You, your wife and daughter all escape a deteriorating containment cell on a distant prototype Halo ring. You are the only survivors. You learn that this ring is special because it represents the most advanced communications and surveillance technology the Forerunners ever developed.
So you're this flood spore, you don't really have a goal in life anymore, so you decide to just find a better life for your family. You do the classic stuff; try and survive in a hostile environment, shelter from the dangers of the Halo ring's malfunctioning weather system and generally try and find somewhere suitable to settle down and live a humble life.
You go about your daily chores: tending to the fire and keeping warm, sweeping the porch of your weird, but respectable flood house, teaching your daughter how to read, watering the plants.
Life is hard, but you get by.
Soon, disaster strikes. Your wife was spotted, attacked and left for dead by a patrolling forerunner sentinel. It flys back to Halo HQ to tell the other sentinels that you're here. You learn from your dying wife that the sentinels plan to self destruct the halo ring.
"You must save Halo" she says as her dying breath.
You and your daughter are now in grave danger. You wanted a quiet life, but you realise the only way your daughter can survive is by infecting the local wildlife, building an army and taking control of the Halo ring.
Of course, this isn't easy. Eons ago - before you were in that containment cell, you were on the front lines of the Flood war against the Forerunners. The tragedies and horrors of war are still on your mind, and this internal conflict has scarred you for life. You come very close to giving up entirely, but you look into your daughter's eyes and see the same eyes of your wife, you must protect her to honour your wife's memory.
Your war is a great success. Eventually, as acting general of this new flood army (the flood spore now has a military badge pinned to it, and a general hat, no explanation) you manage to capture key strategic areas on the Halo ring, including its control room. You prevent Halo's self destruction and you, your daughter and your new friends can now live in peace.
Under your leadership, a new golden age ushers peace and prosperity for the flood, who pioneer exciting advances in the arts and culture. Everyone has impeccable taste and good story tellers are revered in your society. Also, your chief scientist invents a VHS player, neat!
And what luck! This forerunner surveillance array just happened to record the events of the entire Halo trilogy, and it's on VHS! Excited to learn about the history of the universe, you and all your flood friends huddle round to watch it.
It's a tremendous hit!
Everyone loves the Master Chief and Cortana, everything Sgt Johnson says is met with fits of laughter, and of course the Gravemind and his rhymes are a huge hit! There is uproar as you make make a cameo appearance in the background of one of the lore videos whilst fighting the forerunners, as the first flood celebrity you become a hero to your people!
Years pass, there's rumblings that the array has collected enough data to produce not one, but two new movies! And it's true! They both show up in the VHS section of this Halo ring's library, everyone is really excited!
But it wasn't what you expected.
Your daughter...she was so distraught after watching how poorly handled Halo 4 was, that her finely cultured mind could not process it, she jumped off the Halo ring and was never seen again.
Your people (mainly professional art critics) were equally aggrieved.
"Why were they fighting the covenant again? The original trilogy ended on such a beautiful, symbolic note. Why would they restart the covenant conflict and not explain who the splinter faction even were?"
"Why were the characters so horrendously written? I simply do not understand how the awful infinity crew staff could treat the chief in such a terrible way after he literally saved the Galaxy, it doesn't make any sense?"
"What was the deal with the Didact? He was such a boring villain, why would they get rid of the Gravemind for him? I feel marginalised!"
Your people are in dismay. It's now raining because that dickhead Gary from IT has been slacking off and the weather system is playing up again, your daughter is dead, and right about this time you realise you haven't had sex in years because your wife is dead as well.
"Oh woe is me" says the single flood spore to his chief scientist, "what do we do"?
"There is a way" he says. "Our people found something In the library, in between a copy of 'Gears of War - The Musical' and 'Horny Hunters 2' we found a forerunner blueprint for a time machine!
"Oh golly" replies the flood spore "does that mean?!"
"Yes. We can retcon the new Halo trilogy - everything will be as it was before. But the cost is great my lord, to access the rare materials needed for this project we will need to take over the entire galaxy."
Later that night, you sit in your study smoking your pipe, looking over the various photos taken over the course of the original halo trilogy.
"Everything will be at it was before" - you murmur to yourself.
You silently look at the picture of you and your family, your daughter is wearing a Halo 2 t-shirt, better times.
You understand that the consequences of this plan is great. It would mean war once more, the greatest one you have ever fought. Is the cost of enslaving the entire galaxy really worth it just to retcon Halo 4 and 5? Were they really that bad?
"I thought you'd be taller"
The word taller echoes in your mind.
"You must save Halo" - you hear the whisper of your wife's dying words once more.
It is settled.
You storm out of the study and find your chief scientist.
"Prepare us a spaceship my good man!".
"But where are we going?" The chief scientist replies.
You smile, knowing he will understand the reference.
"To war".
Halo 6 - Finish the fight.
-----------------------------
This game would be great, you and your flood army get to destroy and consume everything 343i have introduced into the universe. The Didact, the Infinity, Agent Locke, Sarah Palmer, everything.
The final confrontation would be against the Master Chief, but as you are now the Gravemind you once again convince him to join your cause for the sake of the bigger picture.
In the last scene you play as the chief, you get to make the decision whether to activate the time machine.