- The death of Shiori Kazami (Shun's Mother), the first time you see Shun is completely broken into tears after he sees her deathbed. For unknown reasons, this scene is changed in English version, and the doctor told to him that she's just tired. If you wonder why she'll never be seen again, here's the reason.
- In episode 31, when Shun falls into hallucination of Oberus when and is challenged to fight with the young version of Shiori. It gets worse when Oberus burns Skyress and Shun starts feel saddened, admitting that he needs his friends to move on, and that each one of his friends are important as ever. By the time Shun realizes this, it is far too late. Skyress has perished and Shun mourns over her loss. As drops of Shun's tears fall on Skyress' Ability Card, resulting in Skyress evolving into "Storm Skyress''
- Preyas getting sent to the Doom Dimension in episode 17, and Marucho's reaction to it. What's worse is that both Marucho and Preyas knew it might happen, but Preyas chose to go into battle anyway to make sure the deaths of Marucho's other Bakugan (Limulus and Juggernoid) wouldn't be in vain. Oh, and when he comes back, he's gets corrupted by negative energy, and sends several of his former teammate's Bakugan to the very place he was brought back from.
- From episode 27, Dan's reaction to Masquerade having Hydranoid blast Drago even after he's been defeated. Even worse when Drago is sent to the Doom Dimension.
- What makes it worse is that Dan follows Drago into the doom dimension, while Julie, Shun, Marucho, and Runo watch.
- Drago's reaction to seeing Dan in the Doom Dimension.Drago: What? No! It can't be!
- Even though he has no hard feelings on finding out Alice is Masquerade like the group would, Shun's blunt statement of the revelation is enough to send Alice into tears.Shun: Well, you've proven one thing: Masquerade knew where to find us because you were him.
- The death of Masquerade in episode 44 counts, simply for him being so calm and excepting of his fate.
- All the kids having to say goodbye to their Bakugan partners in the finale.
- Drago becoming one with the New Vestroia's core.
- Wavern's death. The fact that Drago has to kill his love is truly gutwrenching, and Joe takes it very hard.
- Episode 16, Drago getting himself captured by Spectra.
- Episode 17, poor Dan's shock when he sees Drago has been altered both in mind and body by Spectra, even obeying all of Spectra's orders.
- The entire scene of episode 18, wherein Spectra abuses Drago and he starts crying tears due to his suffering.
- Skyress leaving Shun, for the last time in episode 26. After Shun's been busting his butt to save her.
- Volt learning what happened to Brontes during episode 31, poor boy is shocked.
- Episode 32, Volt's desperate attempts to get Brontes back. He fails, worse still Brontes is abandoned by Gus shortly after the battle. Leaving him to cry out (having somehow gotten his soul back) for Volt to save him.
- Episode 52, Mira's cry for her father is heart-wrenching as the Alternative explodes with her and Keith's father inside.
- Sid's death in episode 23, even if he had been a bit of a jerk up to that point.
- The flashback of episode 26 wherein Kazarina fought against the young captain of the royal guard Jin. Who was also none other than Fabia's fiance, the battle resulting his death and Aranaut's capture. It is believed that Aranaut suffered amnesia after being tortured by Kazarina. However, Aranaut was actually lying on Fabia's behalf due to the sadness she felt when Jin died. And at the end of Ren's battle with Fabia, after he realized he was unable to avenge Sid's death, Ren breaks down into Tears of Remorse and Fabia finally accepts his redemption. Allowing Ren to finally got his HeelFace Turn from Gundalia side to the Nethians.
- From episode 28, Jake's torture while being experimented on by Kazarina.
- Episode 29, Dan's feeling like a failure as a mentor for allowing Jake to be captured by the Gundalians.
- Near the end of 32, Nurzak does manage to save Fabia. However, he and Sabator get carried away by the rushing water. Nurzak then has a vision of his daughter as he apparently drowns.
- The deaths of Anubias and Sellon in episodes 21 and 22 were surprsingly tear inducing despite the fact that the pair showed almost zero redeeming qualities. While Anubias was by far the more sympathetic of the pair, watching Sellon plead to live just long enough to see the perfect world her master planned to create was a very Kick the Dog moment for Mag Mel.
Noah: I can't believe I used to look up to you! What a fool I was! I hope that Dan totally crushes you.
- Noah's devastation upon learning Anubias was using him and his teammates.
- From episode 44, after not seeing many of these Bakugan for years, it was great to see Preyas, Elfin, Tigrerra and the like again. What was not so great was watching them all being slaughtered while trying to defend New Vestroia. It was all pretty horrible, but the deaths of Elfin, Amazon, Preyas and Tigrerra were probably the biggest tearjerkers.