Chief is fairly out of it following the events of the last episode, with Cortana notifying him to seek medical attention as his system is completely overloaded due to this contact with the keystone.
As he's both physically and mentally out of sorts, he casually locks Dr. Halsey in her lab, turning on a system modification that will emit a fatal level of radiation into the room. He seems unfazed by this whole situation as Cortana instructs him to stop what he's doing and let her out, with rage building in his body as he remembers bits of his childhood and her involvement in it.
Just as the gaseous radiation is being let into the lab, Chief finally acts and lets Dr. Halsey out with practically zero time to spare. Basically, it was a test to see if Cortana had the capability of saving her, but as she's only able to shut off Chief and not operate him, she wouldn't have been able to step in for the save.
Later on, Chief demands a meeting with Dr. Halsey and they finally get to hash things out, as she had been putting off the meeting for quite some time. She ends up revealing that she did indeed kidnap Chief as a child, along with other children who were trained to become Spartans. Instead of telling the families that she was taking their children away, she came up with the idea to flash-clone the children beforehand, pulling a bit of a switcheroo on them.
As the clones would naturally die off as time passed, the families were left mourning as their real children were actually alive, being trained into Spartans by Dr. Halsey and the UNSC.
With this revelation, Admiral Parangosky (who had been listening in to this conversation) decides to remove Dr. Halsey from the premises, firing her effective immediately and putting her daughter, Miranda Keyes, in her place. However, this exile doesn't stop her and her assistant, Adun, from hacking into the Cortana system and spying in on Chief and the UNSC from afar.