Without a shadow of a doubt, the opening cutscene of the mission Two Betrayals.
After making it through the horrific gauntlet mission known as The Library (infamous amongst pretty much everyone who calls themselves a Halo fan), you arrive back at Installation 04’s Control Room with 343 Guilty Spark. You’re led to believe that firing the ring is the only way to stop the Flood from spreading, but Spark fails to mention that all life in the galaxy will be extinguished once again should this course of action succeed.
John approaches the console, inserts the Activation Index into it and observes the Halo preparing itself to fire.
Then, a flash of light. Guilty Spark is knocked back onto the floor and Cortana stands over you, defiant and angry. She reveals that Halo is a weapon of mass destruction on a galactic scale, that it doesn’t kill Flood but it kills their ‘food’.
“Humans, Covenant, whatever. We’re all equally edible, the only way to stop the Flood is to starve them to death. And that’s exactly what Halo was designed to do – wipe the galaxy clean of all sentient life…”
Guilty Spark confirms Cortana’s statement and then starts saying things which set up a mystery that was finally given its resolution almost 12 years later in the final book of Greg Bear’s Forerunner Saga, Halo: Silentium.
Spark asks John why he would hesitate to do what he has already done, and that the last time the Halos were fired, he asked him that if it were his choice, would he do it?
In Silentium, as the IsoDidact prepares to fire the Halo Array, he speaks to his friend Chakas who he assigns as Installation 04’s custodian and names him Guilty Spark. According to protocol, Chakas has his mind compartmentalised, information and experiences from his former life as a human blocked out of his memory in case he were ever to be captured by the Flood.
“Tell me Chakas, if it was your choice, after all we have seen and survived… would you fire the rings?“
It turns out that the cause of Spark’s madness is the result of his old personality bleeding through. He is struggling with the balance between Chakas, the original personality, and 343 Guilty Spark, the artificial one, and as a result he thinks that John is the IsoDidact who he last spoke to 100,000 years ago.
Two Betrayals is my favourite moment in Halo CE because of how horrifying the plot twist is that the only way to stop the Flood is to kill everybody the parasite can feed on, and how it sets up a number of events that are paid off later in the series.