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. It is strongly implied that Halsey is the mother of Miranda Keyes.

In November 2524 Halsey wrote that she was reunited with "her lieutenant" while attending a conference at the University of Calippus, from which it is inferred that the two became intimate. Four months later she wrote a small side note stating "she will have to answer for making me drink decaf," suggesting Halsey was pregnant. In September, 2525, ten months after her reunion with Keyes, she wrote about experiencing separation anxiety, noting "I guess not hearing her cry wakes me up at night too." Then, 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."

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." Another hint toward Miranda's parentage 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 much sense or relevance had Miranda not been biologically related to her.

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 sent to 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, Vice 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.

Accompanying items

When the journal was recovered from SWORD Base by Beta 5 personnel in 2552 prior to its destruction as part of Operation: WHITE GLOVE, the journal had the following documents and items in it:

Three Intersystem News kiosk tear sheets; "HAVEN TERROR BOMBING KILLS TWO MILLION", "BLISS DECIMATED", and "LCDR MIRANDA KEYES AWARDED SILVER STAR"

DNA sequencing chart of ORION Candidate 047

BIOnano card of SPARTAN-117

Single-image photo of a space anomaly, recorded by a Mars telescope in 2524, accompanied by a note

A memo from the log of UNSC Accra detailing the glassing of the colony of Bliss

An ONI memo regarding Covenant glyphs, accompanied by a photo of the symbols on a Sangheili's armor

Heavily redacted deployment info note of SPARTAN-052, sent to Dr. Halsey by Colonel Urban Holland

A print of a screencapture from a security video of NOBLE Team's operations

Schematic of the Mark IV MJOLNIR PAA

Hand-drawn diagram of the "Keyes Loop"

CAA map of Reach, annotated with Halsey's notes on artifact sites and ONI facilities

Dr. Halsey's ONI security badge

SPARTAN-II unit patch

Partial SPARTAN-II candidate records of SPARTAN-051 (accompanied by a psychological evaluation), SPARTAN-095 and SPARTAN-137.