* A rather small yet still powerful one occurs in Chapter 26, [[spoiler:Garrus and Master Chief get into an argument over Tali almost finding out about Cortana. Garrus tries to pressure Chief into revealing Cortana to the crew, believing that they wouldn't rat him out because they practically revere the guy as a hero, while Chief continues to disagree. A intense argument between the two occurs that keeps building up and up until finally the Chief [[NotSoStoic breaks his normal stoic attitude by practically yelling at Garrus, while almost preparing to hit the Turian.]] He then finally cracks open and mentioning all of his friends, practically the closest thing he had to a family are all dead. And all he has left is Cortana, and can't risk the Council taking her away.]]
-->[[spoiler:'''John-117:''' She's all I've got left!]]
* "I thought we were friends."
** What really makes the above line hurt is that not only does Chief seemingly ignore it, but even the ''narration'' barely acknowledges she said it.
* When trying to work together to restore Peak 15's [=VI=], Tali angrily yells at Cortana about how synthetic lifeforms have made her people's life miserable, citing the fact that she'll never be able to experience normal life due to being stuck in a suit all the time. There's a pause before Cortana speaks.
-->'''Cortana:''' [[NotSoDifferent That makes two of us.]]
* In a happier moment of tear-jerking, the name of a sports team on Reach is the "New Alexandria Nobles." Noble Team, their battle against the inevitable, their heroic sacrifices... they are remembered.
* The Chief goes to visit the memorial on Reach where all the Fallen SPARTAN soldiers are remembered. ''All'' of them- not just the more well-known SPARTAN-II soldiers, but the SPARTAN-I soldiers (including Avery Johnson Junior) and the SPARTAN-III soldiers. Despite their background, despite their differences in missions... all of them are remembered in one place. Guardians of humanity, they rest content, knowing that they did their duty.
* The mental back-and-forth The Chief does as he ponders The Rachni Queen's fate. Most players had an easy time picking one option or the other, but the Chief, as Major Ackerson and Admiral McAllister [[TwoLinesNoWaiting discuss in the same chapter]] is fundamentally ''broken'' and has difficulty empathizing with others, let alone aliens people know little about. The normally decisive Chief flip-flops on a matter of life or death to the point where he almost seems to be on the verge of a HeroicBSOD. His decades of training and discipline coming into conflict with his last few in-story weeks of character development, forcing him into a corner until he finally settles on something and inputs [[AmbiguousSituation some unspecified commands]]. Only an update will reveal what he has decided.
** When we finally get back to him, he tells The Councilors that he killed it, and Sparatus chews him out for it, naturally. [[spoiler: This is a complete and utter lie, however. He let the Queen go]].