- When the Earth Defense Army is doing a data analysis on the recently unearthed Stone-Like in Scene 2, the moment they are about to see its memories it decides to first blow up the 3rd Research Division. Cue (probably the Stone-Like) summoning an exponentially increasing number of objects around the complex while everyone inside is losing their minds!
- The last stretch of Stage 5 "Victim": while the tone of the game is rather sad, what with the crew of the Tetra being the last remnants of humanity and all, but the specific example is the moment where Gai does his Heroic Sacrifice.
- In the epilogue, C.R.E.A.T.O.R. is never able to tell the clones of Buster and Reana about the Stone-Like and change the future. All it did is create a Stable Time Loop; there's no guarantee humanity can be saved.
- The game's premise itself, particularly how it might feel being one of a few Sole Survivors of a race left in the universe in a spaceship that barely escaped the Depopulation Bomb, knowing you're all that's left and next-to-nothing about what caused it to happened in the first place. At the same time, you realize you'll have to return to the planet in a year or so when you run out of supplies. A few humans simply isn't enough to repopulate the human race, thus even if you manage to destroy the Artifact of Doom, there will be nothing but a dead, hopeless planet left.
- The fact that nothing good came out of this entire story: it's all a hopeless Last Stand that ends in a Stable Time Loop as a result of Eternal Recurrence.
Tear Jerker / Radiant Silvergun