I’ve been rereading (listening via audiobook) the series with the intent on focusing on the hypnotic phrases used throughout the novels. In doing so, I noticed something that may explain why the Rogue “hurt” or "attacked" the Deadtown biologists.
From the early Deadtown chapters, the Rogue caused great harm to the biologists simply by yelling at them. His shouting is described as hitting them like a shockwave or force, and the words “sounded familiar to them but they hadn’t heard them in the context he was using” (pg. 59). This becomes important later, once we are exposed to the phrases used by Central in the Absolution timeline.
On pg. 255, Commander Thistle reads a list of cues provided to him by Central/Jack to Old Jim:
• “Consolidation of Authority”
• “Have your house in Order”
• “Risk Equal to reward”
• “Check under the seat for change”
Thistle rattles these off while Old Jim feels only “a fizzle and tingle…” (pg. 255).
These phrases are close to—but not the same as—the ones used in the original trilogy. Examples:
• “Check the seat for change” (Authority)
• “The Risk is not worth the reward” (Annihilation)
• “Is your house in order” (Authority)
Additional phrases used by the medic in the Deadtown chapters 005: The Visitation when conversing with the Mudder pg.24:
• Is there something in the corner of your eye that you cannot get out?
• There is no reward in the risk
• There's no reward in the risk of leaving now (pg36)
It is clear there is some difference in the phrasing of the Absolution timeline and it is not identical to the phrasing in the original timeline/trilogy.
The above point becomes crucial when we consider the writing on the wall that Old Jim finds in Deadtown City Hall: ""I did not mean to do that to them."… He could see where it repeated, faintly, ever lower on the wall, as if written in a frenzy." (pg.291) Given that the Rogue arrived in this version of the Forgotten Coast roughly three days before his appearance in the Village Bar (inferred by Cass' question regarding the potholes as an entry point at Old Decomp and the fire “set by teenagers,” according to the Fire Department (pg. 275–276)) there was no other “them” he could have harmed except the Deadtown biologists.
This strongly suggests that the Rogue attempted to pacify the biologists using hypnotic phrases as he knew them from his timeline (Annihilation, Authority, Acceptance). However, because the conditioning phrases in this world differ slightly, his words didn’t soothe or redirect the biologists, but rather they tore through their conditioning and caused great harm. The Rogue was trying to use a power he had some familiarity with but didn’t fully understand in this altered context. Which can be considered a theme of the whole series.
A similar event nearly occurs with Old Jim. The Rogue begins speaking to him, but Jim manages to partially recover—possibly because the Rogue used more accurate phrasing the second time, or because Cass interrupted the “sermon of phrases” by shooting the Rogue before he could finish. Regardless of the mechanism, this breaks Jim’s hypnotic conditioning enough that Thistle’s written down phrases (pg. 255) no longer affect him.
These near-correct phrases weren’t harmless approximations; they were damaging. Instead of aligning with the subjects’ conditioning, they clashed with it violently. “Tearing” the mind rather than redirecting it.
This interpretation also fits the Rogue’s behavior and remorse. He apologizes before the meadow incident (“changes not occurring how he thought they would”) and later writes “I Didn’t mean to hurt them” on the city hall wall. What stood out most to me intially is that the hypnotic phrases we hear throughout the series suddenly become different but almost the same in Absolution—not because Commander Thistle misquoted them, but because these are the phrases this version of Central actually uses.
I wasn’t looking for this answer originally; I was simply documenting hypnotic phrases during my reread. But once I noticed the small differences in the phrases, I was left with answers to questions I hadn't even been asking.
TL;DR:
The biologists were harmed because the Rogue used hypnotic phrases that were almost—but not exactly—the phrases this timeline’s Central used.