As Makee isn't giving in to Dr. Halsey's request, Halsey goes rogue and sends out a direct order only to three Spartans (Kai, Vannak, and Riz) to locate Chief, Makee, and the keystone and to bring all three back to her ship, where they'll take off for who knows where. This is considered the "Zed Protocol," which is put in place when the senior leadership of the UNSC isn't making the right decisions (which isn't true). Honestly, I don't know why they're even following her instructions given that Halsey has been fired.
Well, all except one decide to follow her protocol; Kai—as she has removed the chip from her back—doesn't feel right about these instructions, which she verbalizes to the others. Hearing this, Halsey secretly orders the other two to kill her, yet instead, they knock her out and tie her up against a pole to prevent any further action.
Knowing that Chief won't go along with this plan, Halsey instructs Cortana to disable him as she did once before, though she seems a bit skeptical of the whole thing.
Despite the fact that Dr. Halsey is technically Cortana's creator, she really serves to protect Chief, and it's no more evident than in this moment when she finally disobeys Dr. Halsey and clues Chief in as to what's actually going on. It's a bit hard to get her point across at first, as Chief tells Cortana to shut up and leave him alone (major teenager vibes), but when she yells for him to stop everything, he finally listens.
"Halsey initiated the Zed Protocol," Cortana says. "You're walking into a trap. Turn around and get out now."
Watching along from the monitors, Halsey notices that John and Makee have stopped walking, and it's at that moment that she realizes Cortana has betrayed her. To be fair, this shouldn't come as much of a surprise to Halsey as she treated Cortana like total garbage for the majority of the series—this was a loooooong time coming.
Although he was warned, Chief ends up being attacked by the two Spartans and basically gets his butt majorly kicked. Just when it seems like they're going to fully kill him, Kai swoops in, having broken herself out from being cuffed to the pole. She doesn't help much, though, as things end up in a stalemate with basically everyone pausing and pointing a gun at one another.
In another room, Makee has been taken away to be with the higher-ups at UNSC, attempting to get them to take the threat to the Chief's life seriously. They decide not to listen to her and instead proceed to tase her repeatedly, which eventually drives her into a rage great enough to reach over and touch the keystone. As we've seen before, this sends a massive shockwave through the building, and Chief is thrown back into the calm meadow from before. End scene.