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Tear Jerker: Homeworld
The life on Kharak pre-Guidestone discovery consists of Kiithid (clans) beating the crap out of each other, fighting over already scarce resources or their own ideology and belief which turns out to be wrong. From a race punished for a great crime devolved into disillusioned people fighting for a past that they don't even remember anymore.
The Mothership returns to Kharak, expecting a safe return for emergency repairs, only to discover that the scaffold, Kharak and its 300 million inhabitants you knew so much about in the manual, were wiped away by fire. The initial camera viewing angle given to you is cleverly placed facing away from the burning planet to maximize the shock value towards the player when the player proactively turns the view from the wrecked scaffold to the burning world below. Cue Agnus Dei (the choral version of Barber's Adagio for Strings).
Throughout the first few lines of dialog between Karan S'jet and Fleet Intelligence, both well-known for their unbreakable Danger Deadpan professionalism, tones of devastation, desolation and despair can be heard, showing that even the hardest individuals are barely holding it together.
Fleet Command: No one's left. Everything's gone. Kharak is burning...
Fleet Intelligence:The scaffold has been destroyed. All orbital facilities destroyed. Significant debris ring in low Kharak orbit. Receiving no communication from anywhere in the system... not even beacons.
Moments later, a glimmer of hope shines through: the Cryo Trays are still intact but sustaining damage from a Taiidan mop-up group that stayed after the attack. The mood of the dialog from Fleet Command and Fleet Intelligence evokes you to save the Trays like you were saving your surviving loved ones from certain death.
There's another heartwrenching line in that level: You've loaded the remaining Cryo Trays on board, the ship is powering up to jump away and then you hear this:
Fleet Intelligence: There's nothing left for us here. (sigh) Let's go.
After the Kushan save the Bentusi from the Taiidan Empire, the Bentusi see fit to share with them information that was forbidden from being shown throughout the entire galaxy. What information is so important and so illegal that it requires saving the lives of the most powerful alien race in the galaxy to be shown? The exile of your ancestors from Hiigara. The entire sequence is shown as an entire fleet of prison ships making an unplanned and perilous journey across the galaxy on slow, shoddy, unreliable conventional drives, resulting in generations after generations of Hiigarans living as nomads throughout space until they reached Kharak, lying on the edge of the galaxy. Some prison ships don't even make it that far, helplessly succumbing to poor engineering. Others would desert the convoy and decide to live elsewhere, resulting in the cultist Kadeshi. Like the Return to Kharak, this entire sequence goes by with the helping hand of Agnus Dei, which serves to emphasize the undeserving consequences who the Kushans, now innocent and unaware of their heinous past, face as punishment for the sins that their ancestors committed. The entire legacy and future of the Hiigarans and their Kushan descendants is just one big tragedy, which becomes all the more reason for you to help them see it through to the end.