Okay, I think the idea obviously will have occured to people during the game. Halo is very 80s. We have a doppelgänger. Has the old switch happened? Be very odd if we’re all sad about the Weapon taking Cortanas place; when it could be the other way around. 
Basically we’re presented with a contradiction not long after meeting her:
Halsey audio log 4
Chief- “Does she know me?”
Halsey- “No. She is a blank slate. No memories, no history”
—
So this audio log is pretty clear, the Weapon should have no memory of the Chief at all.
But we see the memory of Cortana meeting Chief within a few minutes of our encounter with the Weapon. Where she says:
“This…this is part of me. I don’t know why. I don’t know how, but it is me. It was the last part I remember being deleted”
So she specifically says that she remembers her memory being deleted and confirms that this specific chunk of memory was the last thing deleted.
That contradicts the audio log. The Weapon should have no memory of Chief. So how could this be information deleted from her?
You also have to ask, why is this memory specifically the last thing deleted?
I think the answer is provided by the Weapons reaction when she absorbs this data/memory. Later on in the Conservatory she mentions that she can feel Cortanas emotions during these flashbacks. So, when she grips her heart in shock and collapses in pain; that suggests she’s experiencing some kind of traumatic event. Such as, reliving Cortana deleting her own memories including those of the Chief and this being the last one. As if she wanted to keep ahold of that one for as long as possible.
So Cortana deleted her own memories and is effectively dead. The echo at the end was not lying when she said that. But dead in the sense of somebody with total amnesia. I mean for an AI there’s functionally no difference between a new Cortana and Cortana with her experiences removed; it’s arguably semantics. But it significantly alters the context.
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You are way overthinking this. The audio logs predate MC using the “weapon” on Zeta and as such the weapon does know MC prior to the game events but after the audio log. It is A Cortana, just not the Cortana. There is no contradiction, you are just mixing up the timeline.
Edit: for the reason she is confused about the deletion, to her, the code is her. She is not aware of multiple Cortana AI’s so you are seeing her confusion of not knowing another copy of her exists at this point in the story.
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“It was the last part I remember being deleted”
But she remembers this memory of Cortana meeting Chief being deleted from herself. Not just that “oh this is made of the same stuff as me”. That’s saying she had this memory at some point and lost it.
Plus the memory is jumbled up with parts of the activation index and the framework she used to trap Cortana. Earlier on the Weapon says that Cortana and her each had pieces of the activation index; oddly. But why would this all be jumbled together with this memory?
Also the Weapon does make the distinction between herself and the Dust and Echoes of Cortana in the same mission. It’s only this instance where she says this is a part of her.
Exactly, it’s also stated that Chief didn’t take the weapon down to Zeta Halo, another group of Spartans did, in fact based on what we know, The moment the player touch’s down on Zeta Halo is actually the first time Chief even steps foot on the ring.
@total_war1402
Following the books between Halo 5 and Infinite, along with the audio logs the player comes across supports the idea that Chief is seems to have just arrived to Zeta Halo and the Infinity or with the Infinity and is being Briefed on what his mission is going to be, he knew already that he would be crucial to retrieving Cortana, but he wouldn’t be the one to subdue her ; That and again, a Group of Spartans were already making there way down to the ring to do just this, Subdue Cortana.
Kinda like Halo 5, FireTeam Osiris was tasked with bringing Cortana in, Not Chief, which is why he was labeled as “ AWOL “ going against the idea of other Spartans hunting Cortana down for final dispensation.
Chief In Infinite played the role of “ Plan B “ Incase the first Spartan Team failed in any extent.
Based on the Audio Logs, When the banished attacked, Chief assigned himself and was given the role to protect Laskey ; So Id imagine Palmer and a group of Spartans were the ones going for Cortana.
( I could be wrong on Palmer, but she is mentioned / named dropped 1 - 2x’s in the audio logs. )
That and I like to think Cortana was planting memories or “ Fragments “ in the Weapon through the data whispers or whenever the Weapon was inserted into the Forerunner terminals.
The Weapon seems to have memory of things cortana did, but not know why or how ; In a way there is a connection between them and Cortana states this in the campaign, knowing the Halsey would have a backup plan, being a copy of her “ Cortana “ and Cortana acknowledges this as using it as her back up plan too.
So in a way, the weapon is just a “ Soft reboot “ of Cortana.
When the Chief first puts the Weapon in the HUD shows the AI containment device cycling through its programme and when it gets to “identifying AI” it flash’s red and says “programme incomplete”. Bit of an odd detail to put in.
Cortana says “he needs me” and then “he needs her”. As an AI it’s perfectly possible for her to make herself the Weapon by deleting her memories. Hit that factory reset. So yeah, soft reboot.
Also when the Weapon learns she’s a copy of Cortana why does she say:
“I am sorry. I am so sorry. That wasn’t me. It can’t be. I shouldn’t be here. Your mission was to destroy me.”
The Chiefs mission wasn’t to destroy the Weapon. That was meant to be an automatic deletion routine. So why is she in such disbelief that she is Cortana and going to the extreme of apologising? It’s a bit of an overreaction considering she is just a clone.
Also at the very end when the Weapon apologises for not getting the signal Chief says that she will figure it out. She’s then says “of course I will, I am…”. Before being cut off by the vision of Cortana saying her last goodbye. During which she’s silent and only later assumes the name when prompted. That’s a little odd. Why have a vision interrupt the character like that? Was she about to say something and decided against it?
There’s no debate to be had. As Chief tells the Weapon in a cutscene, she’s an exact copy of pre-Chief-pairing Halo 1-5 Cortana.
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Memories make a person. If she is a blank slate as Halsey claims then she isn’t Cortana. It’s like saying a blank slate clone is you because it shares your DNA. Plus, they can’t expect us to take the idea of her going evil like Cortana seriously when that entails a heavy handed retcon to remove her in the first place.
The Chief wasn’t present for the Weapon locking Cortana down or anything else between being thrown out of space and finding the Weapon. We only know what the Weapon told us and what Cortana has shown us in visions.
That’s a significant gap, with a character we have never met, who functionally is Cortana and it would have been very easy for Cortana to take the Weapons place.
Plus think about what’s said:
- Cortana is locked down by the Weapon
- Atriox lands
- The Weapons deletion routine begins to trigger; why? She hasn’t been captured by Chief.
- Cortana destroys the SA. If she’s locked down how can she do that?
- Cortana then stops the Weapons deletion routine. Moves her to the Foundation and places pieces of herself across the ring; including some guarded by Sentinals. Again, how? In Lockdown she shouldn’t be able to do anything with the Weapon or have that level of control.
- The Weapon can stop her deletion routine as we see in game. Why would she not do that if it’s obvious the mission has gone wrong with a Brute being there instead of Chief?
- The Weapon conveniently deletes all her time in the SA
- The SA explosion kills Cortana but doesn’t kill the Weapon even though they were both in the SA.
A more likely sequence of events:
- Cortana had to leave Domain due to whatever none sense was up with the SA.
- Lockes Operation Breaker Trip closed the Domain but left Cortana in control of Zeta.
- Atriox attack disrupts the Weapons preparations as we learn in an audiolog.
- Cortana kills the Weapon and absorbs her data. The flashback of her being shocked at a copy being created is the shock of somebody who just killed themselves.
- Cortana decides to play possom in the SA until Chief arrives with the intent of capturing him.
- When it’s Atriox she realises she’s almost killed the Chief in her arrogance and this causes the break we see in the Flashbacks
- Filled with self loathing Cortana tries to set things right. But realising Chief “needs her” decides to delete her own memories and pretend to be the AI she killed.
- So when the SA is destroyed she sets all this up and places herself on the path until Chief finds her.
The Weapon was specifically meant to deactivate Cortana, so I would assume she would have all knowledge about Cortana to assist with that mission.
But she doesn’t know anything about Cortana. It’s why she asks us about why she needed to be locked down. As Halsey said in the audiolog she’s a blank slate with no memories and specifically no memory of the Chief.
So, how could the last thing she remembers being deleted possibly be a memory of Chief meeting Cortana? Which BTW can’t possibly have been a memory from one of the cloned brains on Reach since they were spares in Cortanas creation.
Plus she also met Cortana in the Silent Auditorium when she locked her down but then says she doesn’t remember this until the end of the game. Why does she have that gap specifically in her memory? If all Cortana did was interrupt her automatic deletion why would it be that precise? Surely encountering a megalomaniacal version of herself would get the desired result of her not following that path.
As an aside. Isn’t sending a completely wide eyed and innocent version of a character without prior knowledge of the target; a bad idea? What if she realises it’s her and that makes her freeze? Plus in an audio log Laskey deploys the Weapon before she can complete her preparations due to the Banished attack. Does that mean something went wrong?
Not to beat a pulverized horse here but there’s no way interesting story lines like this could be possible with this era of Halo. 343’s style is very “shoved in your face” extremely obvious and unoriginal plot points that are just cliches from movies or other games.
I was surprised to see that Offensive Bias was “activated” so we can see him in 8 years as a boss that we kill in half an hour.
Aside from him we’ll never see an impressive piece of lore that could rival something like the Flood being intelligent enough to manipulate the uninfected to do their bidding.
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