- On the Incan Gold Ship, discovering that the people you've just met have actually been dead for centuries and never got to take the trip they were dreaming of.
- In Larai Cliff, finding the skeleton of an adventurer with a note from his children wishing for his safe return. And much later in Watermia, you can find his children who have no idea he's dead, and are still expressing hope that he'll return. You just couldn't have the heart to tell them otherwise, either.
- Just before the final boss fight, you're transported to the roof of Babel Tower, where you meet with the pure souls of people you met throughout your adventure, including Seth, Hamlet, and your opponent from Russian Glass, who laments, "Living with a terminal illness was better than this,"
- In the Native's Village, Hamlet's Heroic Sacrifice. The game was retranslated by fans, and resulted in a very different portrayal of the Native's Village. In the original translation the Natives were starving to death and the skeletons around the village were those of the villagers who starved to death. While still heroic, Hamlet's actions seemed rather random. In the retranslation, the Natives had resorted to cannibalism due to the famine, meaning Hamlet throwing himself into the fire had a bit more purpose; he did it to save Kara and the others from being eaten. What's interesting is that the cannibalism is portrayed in a sympathetic and sad light. They're not monsters, they're people desperate to survive, and doing the absolute last thing they want to do to live. The boy who shows you a skeleton with tears in his eyes in particular has a whole new meaning in this translation.
- Ishtar's fate. After you go through his Secret Test of Character to retrieve the antidote that will restore Kara to normal, you go back to his room to find him sealed inside his newest, final painting - a self-portrait. He doesn't tell you why he did this, only that you must take care of Kara.
- The backstory of your opponent for Russian Glass. He's a longtime champion of the game, but is secretly suffering from a terminal disease. When you face him, he's gotten to the point where he's playing to lose, so that his family will live a comfortable life with the money he accumulated from years of winning. The next morning when his now-widow gives you his will, she also leaves you with a single message that puts the icing on this Tear Jerker cake: "We don't need money. Real joy is being with those you love."
- In another early location, it's mentioned that the luxurious carpets in Edward Castle take forty years to make. In one of the last areas of the game, you visit the town these carpets are made in. It's revealed that the female workers spend their entire lives making these carpets by hand, from their childhood to adulthood.
- The ending, oh that ending. Just as it seems that Will and Kara have earned their happy ending, they are told that, with Dark Gaia gone, the world was turning back to what it would have been without its influence. That is: history itself was being rewritten, and when they returned to Earth, not only they'd be separated, they would not retain any memory from this timeline. Of course, they do not take this kindly, and defiantly promise to remember and search for each other. (It does work.)
Tear Jerker / Illusion of Gaia
It's pretty safe to say the entire game is full of Tear Jerker moments.