The Equestrian Equation:
- Twilight, upon realizing that her world is a simulation and that she can't trust anything she knows to be real, has an emotional breakdown and needs to literally hold onto Shepard for support.
- Twilight having a bit of a breakdown after brutally defeating Milligan.
- Twilight and Celestia share a tearful goodbye in the Harmony Core chamber, moments before the Awaken Protocol is to be launched. When Twilight is momentarily distracted by the control console, the Princess turns, walking away as her hologram projection fades to nothing. Her last words are: "Goodbye, my little pony."
- Despite Shepard and Twilight's success in rescuing all of the Equestrians, Granny Smith dies soon afterward because she is simply too old and frail to survive for long outside the tanks that held their physical bodies.
- Just the fact that the Equestrians were ripped out of a happy, peaceful life and were suddenly thrust into the frequently harsh and demanding galaxy of Mass Effect with little more than enough general information to get by suddenly jammed into their heads. Not to mention suddenly waking up and finding that some of the friends, family and neighbors that you grew up with your entire life were nothing more than programs.
Shades of Twilight:
- The schism between Twilight and Applejack over the latter's abduction of Dr. Hern from the hospital. Applejack accuses Twilight of betraying her when Twilight insists on informing Lt. Pyres of the situation, and though she tries to apologize after both Twilight and Pyres do everything they can to protect both her and Patricia, she's burned so many bridges with her behavior that Twilight just gives her the cold shoulder.
- Which according to the Equestrian Codex, like the Amish, is considered one of the worst punishment one can face within the Herd, imprisonment being just adding salt to the wound.
- New Ponyville is attacked by a series of firebomb detonations, and eight ponies (including Scootaloo) are abducted while the ensuing chaos has everyone distracted. When Rainbow Dash goes after the abductors, she is subjected to a brutal Curb-Stomp Battle by an Asari Commando which ends with her getting shot in both wings. The only friendly close to her is a changeling drone that can either be ordered to follow the abductor's ion trail, potentially leaving Rainbow Dash's wings crippled if her wounds are left untreated, or try to get her immediate treatment knowing that there's no one else in a position to follow the trail before it goes cold.
- The aftermath of this. Rainbow Dash is fully aware that she failed everyone. It's also clear she'll likely never fully recover her flight, if at all, meaning she's lost her most vaulebule, defining trait. She clearly at her lowest and while she gets better emotionally, it's still a damper on an otherwise happy ending.