Gravity Circuit: Part 11: Ark Assault at Guardian Corps HQ
Regardless of whichever Rebel Circuit you chose to hunt down as your 8th and last one, something... tragic happens at Guardian Corps HQ as that Circuit is brought back, but before Kai follows in with it.
The situation of Kernel having... something try to take control of him... IT FINALLY BROKE ALL THE WAY THROUGH!
Kernel lost his hat, and was just no longer the leader that Pat saw him as. He now just wanted to... "Obey"...
Nega walked in just in time to see Kernel's transformation... And then Kernel SCREAMED and ATTACKED!
When the damage was done, the sounds show that two people teleported out of there...
And then the Ark that everyone was wondering about this whole time... it finally activated...
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When Kai finally returned back to HQ, he was greeted with a wrecked version of itself and a terrified Pat. When Kai asked Pat what happened...
Pat revealed to him that Kernel suddenly attacked and stole all of the stored Circuits. He was now on his way towards the Ark, and Nega was in hot pursuit of him.
Kai suspected that the Ark was the true source of the Virus Army, and that he now had a plan to head there to see how he can finally put a stop to it all, and possibly bring back Kernel in one piece.
In the meantime, Pat will take over with teleporting Kai to any stage he wants to. You can still talk to him to check on your Challenges/Achievements, though.
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Since Nega is gone, he'll no longer be the one to sell you his Burst Techniques. Instead, he has assigned that job to Nurse, who will tell sell you her Enhancement Chips, as well, presuming you've gained enough Rescue Tokens for them. If you have found every Civilian, then you should have enough Tokens to buy every Chip.
From this video, I just came from defeating Hash, the Cipher Circuit. If it weren't for the plot twist I triggered at this point, Kernel would've instead have been relieved that Hash won't be able to get into his personal files anymore, while Nega would've talked about just how much Hash was always full of himself as a Circuit with incredible computer capabilities that has tended to lead him to be more of a burden to the other Circuits rather than an asset.
Also with this, if you found the Palette Chip of Cipher Circuit's stage, you can pay Prim to give you the Scheming Pink alt color, which lets you wrap and teleport through solid objects, but only for a couple of seconds and then it will need more time than that to recharge. Back on the Nurse just for this playthrough, you can gain Clone Array and Hologram Trap from her after beating Hash.
The NPC you can talk to if you found them from Hash's stage is another bookworm bot named Tech. He has a lot of knowledge about the cyberspace that Hash spent a lot of time in.
Going forward, every NPC basically has their own thoughts on how Kernel has apparently "betrayed" the HQ one way or another. The only thing to do from there is to just push forward, head for that Ark, and see what REALLY went wrong with him...