WARNING: UNMARKED SPOILERS BELOW.
- Final Flight of the Osiris: It's right there in the title. The crew of the Osiris collectively perform a Heroic Sacrifice fending off an attack from Sentinels while Jue performs a risky drop-off inside the Matrix to inform Zion of the Machines' plans putting the events of the tie-in game Enter the Matrix and The Matrix Reloaded in motion.
- The Second Renaissance. The entire story, period. It shows that the machines had a very good reason to become the way they are now. The most horrifying part is the scene where the humans essentially commit genocide on them, throwing them into pits like dirt, rounding them up like animals, beating them to death and more.
- Though their reasoning for going to war with humanity is sound and just, seeing how quickly the Machines devolve into nightmarish monsters just as bad as their oppressors is horrifyingly tragic. Humanity broke the Machines, so the Machines broke them right back.
- At the ending, the Instructor just caressing a pod containing a small crying child. It really hammers into you how the Machines enslaved humanity.
- World Record doubles as both a Tear Jerker and an Awesome. At the end, Dan Davis is left crippled having broken his own 100m record and temporarily escaped the Matrix through sheer willpower. As he's being pushed in a wheelchair by a nurse, he starts mumbling "free" and stands up, snapping his metal leg-braces in the process, again all through sheer willpower. As an observing agent starts to tell him to sit down, he begins to levitate before finally dropping to the floor, all to a soaring, heartrending score.
- Matriculated: A lone machine is reprogrammed by a small group of Resistance fighters to join their cause. The rebels are soon killed by an arriving group of loyalist Sentinels, despite the rogue machine's attempt to protect its new friends by destroying its brethren. It then tries to save the last dying human by plugging her into the artificial world, only for her to choose death instead and leaving it all alone.
- Program: Cis kills Duo, who then tells her that he loves her, causing her to do a Big "NO!" until the medieval Japan simulation turns out to be a program. This is one of the happier endings out of all the shorts.
