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.
Pi's death, and the subsequent devastation it wrecks on his boyfriend, Joseph, one of the happiest characters in the RP.
Locke getting brutallycurbstomped by Wesker the Whisperer. For one thing, this man instigated the murder of Locke's parents. Locke had been training and making himself stronger and did his best to get into the International Police because he wanted to hunt down Wesker and beat him, and Wesker renders all of those years' hard work for naught in a matter of minutes,(nothing Locke does even fazes him) and then separates Locke from Geo and Denise, his Lucario and Arcanine respectively, who are two of his closest friends, by having his Gallade teleport the two away, and Locke has no idea where. By the end, Locke has possibly lost two of his best friends, had his leg broken, and his dreams crushed.