Dr. Halsey's personal journal is a booklet co-written by Eric Nylund and is included with the Halo: Reach Limited and Legendary editions. It covers various elements from the Halo universe and is written through the eyes of Catherine Elizabeth Halsey herself.
In the journal, several important revelations are made regarding Cortana and Halsey's relationship with Captain Jacob Keyes and Miranda Keyes. Halsey states in an indirect fashion that she and Captain Keyes had a relationship and that though Halsey had been close to Miranda, they had drifted apart.
Furthermore, it is stated that when Miranda received command of her first ship, UNSC In Amber Clad, she had invited Halsey to attend the ceremony but Halsey refused, stating, "I didn't go. Because her father would be there? Because I am neck deep in the final stages of a half-dozen projects? I know why I didn't go. I don't want to say it." From this it is inferred that Halsey is the mother of Miranda Keyes. Another clue to this theory is that Halsey wrote in the journal that Miranda had her surname changed to "Keyes", which she believed was done to try and impress her father. It is also mentioned by Halsey that Cortana's appearance somewhat resembled Miranda. Since Cortana was derived from Dr. Halsey's own brain, this remark would not have made much sense had Miranda not been biologically related to her. Finally, on July 12, 2531 on the side of the page, Dr. Halsey wrote, "Jacob has agreed to take her in. I'll miss her, but it's for the best."
The journal also provides an explanation of why Cortana was seen on Reach as well as mentioned in Halo: The Fall of Reach, assisting John-117 and his team of SPARTANs on their mission. It seems Halsey needed to analyze the Forerunner symbols and systems in Professor Sorvad's site. Halsey and Cortana both independently figured out the "Solomonic solution" which helped "divide" Cortana and allow "parts of her" to help Halsey while updating her "incarnate" self on the UNSC Pillar of Autumn until the last minute. The two parts were reunited sometime after Cortana's fragment was delivered by SPARTAN-B312 to Captain Keyes before the Pillar of Autumn left Reach.
It provides an explanation for the inconsistent numbers of Spartans, particularly involving those not present during the Operation: RED FLAG briefing. Halsey states, "That lie about all the Spartans gathered here, save for Gray - will that come back to haunt me?" Halsey notes that the bodies of the candidates who were killed during the augmentation procedures were placed in cryo-stasis, with the possibility that they may some day be resuscitated, though they appeared to be buried in space. She also notes that at least some of the candidates who were crippled could some day be rehabilitated and put on active duty.
The journal also confirms that Dr. Halsey was aware of the existence of SPARTANs who were "not [hers]" well before the events of Halo: First Strike. She and Kalmiya had uncovered numerous ONI documents and encrypted files that suggested the existence of another SPARTAN program. After the UNSC Hopeful was deployed outside the Epsilon Eridani system for a week, carrying various "carcinogenic", "mutanogenic", and "experimental" drugs. Upon his return, Admiral Ysionris Jeromi informed her that he knew little of what was going on, and could tell her nothing. Finally, Halsey reveals that her suspicions of other SPARTANs were confirmed when she met Noble Team at Sword Base. Later, at CASTLE Base, she discovered that they, with the exception of Jorge-052, had been SPARTAN-IIIs.
- The journal is missing two pages, of which the content and date of removal are unknown. She tears these two pages out herself when she finds the journal during the events documented in Halo: First Strike.
- The two missing pages are found in the seventh section of the diary.
- Halsey's journal can be found on the mission "The Package" in the Tribute Room.
- The journal interestingly mentions a concept for MJOLNIR Mk VII (a reference to the number 'seven') which later becomes the Mjolnir Generation 2.
- The pages in the journal are exactly seven inches from top to bottom. This may have been in order to fit the journal into the case. It is also a reference to Bungie's favorite number.
- Halsey's journal would be recovered by Margaret Paragonsky and read by several current and wash out Spartans.