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We Are All Pokémon Trainers
Giratina being forced to watch Cynthia, the one who hatched its egg, die in a fire.
What Missingno turns out to truly be.
Rebecca abandoning the group and the consequences that follow.
Anom's Yanmega getting eviscerated and hung in a tree by the same pack of Zoroark that nearly killed her trainer.
Daisy's Audino Pink getting blackmailed by M into splitting the group up or he would harm her family and get turned into a glitch. The sad part is, she
does get turned into a Glitch Pokemon Portales' entire backstory.
The apparent deaths of Jane and Wolf, and the others' reactions to it.
Heroic Sacrifice and how it affects the other trainers. Jane's breakdown.
Various young Pokémon in Pinwheel Forest in the alternate timeline arc being orphaned as a result of the battles against Scolipede and Artemis' minions.
Unite's Despair Event Horizon upon thinking that Woolly was killed by Barb the Beedrill.
DS' Sinnoh team believing that DS is dead, with the exception of Briar Rose, who is upset by the fact that she is the only one who believes DS is still alive.
The entire flashback sequence showing what had happened to DS in the beginning of the AU arc, starting with DS' reactions to everything that had happened, and ending with her seemingly being killed by Primal Dialga.
getting in the way when Napoleon tries to stab Artemis, being fatally wounded in the process. Mira manages to live long enough to give Artemis a Dying Declaration of Love before dying. Sol's death in the AU. She tells her parents that she'll be careful when she goes into Route 123. She gets captured, tried, and executed.
People saying their goodbyes during the climax of the Hoenn arc, in which Mt. Pyre's eruption threatens to not only destroy Hoenn, but the whole of Pokepan. Highlights include:
PMD-B Gamer/Joshua's death.
Celzvet's last will and testament to Sagi during Conquest, due to the former being forced to fake his own death.
Diane's . Also counts as Shadowfication Nightmare Fuel.
Des's death and subsequent farewell to Sakura. Subverted in that Sakura didn't cry, just as Des asked her to do. Crewe
finally getting her memories back upon being purified, and then realizing she accidentally fatally wounded Straw moments before when she went into Reverse Mode.