The actual episodes already had many sad moments, but the extended fic adds them a lot.
- Twilight reveals in the second chapter to Jewelius that she's planning to sing "Love is in Bloom" during the wedding reception, and she ends up singing it along with him. Then the entire wedding rehearsal incident occurs in the third chapter
- When Jewelius grills Shining Armor in the fifth chapter, the prince asks whatever or not it was entirely Chrysalis' fault that the captain disowned his sister for trying to warn him. The ashamed Shining Armor ends up admitting that Chrysalis had no influence over that decision of his. Twilight makes a heartbroken expression as her brother hangs his head.
- When Celestia is subdued by the Royal Guard, the wedding guests do nothing but glare resentfully at their once adored ruler. Crestfallen because of this, Celestia wonders if she's going through the same feelings as Twilight (who's at the time lying unconscious on the floor) did at the rehearsal.
- Suddenly losing her authority and prestige because of her nephew using her failures to denigrate her is implied to be such a shock to Celestia that she turns despondent. When she and the other disgraced heroes are sentenced in the next chapter, she remains silent for the entire scenario while her sister and the others try to speak for their defense.
- In the 15th chapter, Celestia has become low-spirited due to everything that's happened so much that she's starting to be afraid Twilight is too much wrapped in Jewelius' influence. Cadance has to urge her not to give up on the hope of her faithful student coming around.
- When the heroes' failed escape attempt succeeds in making them look as guilty as Jewelius says they are, the wedding guests do nothing to help them and only look at them with disdain as the guards take them away.
- When Jewelius sentences them to slavery, the Mane Five resort to tearfully begging for mercy.
- While he's being transported away from Canterlot, Shining Armor laments over being separated from Cadance, Twilight and his parents. He also laments not being allowed to know if his sister (whom he last saw falling unconscious) is alright or tell her how sorry he is for renouncing her.Shining Armor: I could've gained a wife. But instead I just lost a sister.
- Anytime Celestia, Spike, Shining Armor, or the Mane Five express remorse over shunning Twilight and inadvertently letting the invasion to happen. Celestia and Shining Armor also beat themselves over being unable to realize Cadance was imprisoned underground and impersonated by an imperfect impostor. Shining doesn't even care to excuse any of his actions with Chrysalis' mind-control spell.
- Jewelius sends Spike the wedding cake toppers and Rarity her bridesmaid dress to pour salt in their wounds and remind them of the failures they were banished for.
- Cadance telling everypony how Twilight secretly helped her and Shining Armor to become a couple years ago makes Shining Armor feel even more horrible about banning Twilight from the wedding. Cadance is understanding instead of angry with him, but when she asks him to reconcile with Twilight before they get married, it means in his mind that his relationship with the mare he loves depends on his reconciliation with his sister. The revelation of Twilight being a Shipper on Deck toward her big brother and foalsitter since her fillyhood also makes the Mane Five better realize how utterly selfish their own behavior was during the wedding preparations.
- The lashing out Twilight gives her brother, friends and mentor in the 10th chapter. They came a long way to make amends with her by saving her from vengeful Changelings, and she bitterly renounces them as payback for how they treated her at the rehearsal. The point's driven home with their own parting words from the rehearsal thrown back at them. It is for Shining Armor a confirmation of what he has been fearing ever since his banishment; that his once great relationship with his little sister has been ruined because of him.Applejack: Twilight, please don't do this!
Fluttershy: We're your friends!
Twilight: No you're not! You only hangout with me because my connections could help you. You never cared about me or anypony else! I can't believe I fell for it for so long.
Shining Armor: Twily-
Twilight: And you can forget about me calling you my BBBFF anymore! In fact, I don't even have a brother. Now if you'll excuse me, I'm going to go check on the princess.
Celestia: Twilight, I-
Twilight: You have a lot to think about.
- What makes this worse is that Cadance just got injured and Twilight, mistakenly believing the others caused it by bringing her to Canterlot before Jewelius could reinstate hernote , is calling them out for that. Though she was not happy about seeing them due to Jewelius corrupting her against them and responded with annoyance to the rumors they had heard about the Changelings chasing her, she didn't lose it before she found her beloved foalsitter lying injured on the floor.
- The revelation that the large number of royal guards who were injured by the Changelings yet remained loyal to the dismantled princesses were murdered on Jewelius' orders, with their relatives tricked into thinking they were casualties of the invasion that was their dismantled captain and Celestia's fault. Celestia and Shining Armor are utterly shocked by this (the latter had many friends in the Guard), feeling some responsibility over the fate of their murdered loyalists.
- In the 12th chapter, as everypony waits for Celestia's hanging to commence, the chained and disgraced heroes suffer insults from Canterlot's citizens who blame them for what they suffered because of the Changelings' attack as well as everypony who lost their lives. Nothing the desperate heroes say can convince anypony that Celestia's hanging is wrong and that Jewelius is the true villain. Twilight herself doesn't really like to have Celestia hanged, but she claims that she has done all she can to help her former loved ones. Unfortunately, her friends and brother's attempts to make her listen to reason only upset her to the point that she snaps, screams a Big "SHUT UP!" and bursts into tears. This angers the crowd who sympathize with her even further.
- Lyra Heartstrings, Minuette, and Twinkleshine call the heroes out for not caring about their disappearance and the Mane Five of shamelessly replacing them as bridesmaids. Shining Armor thoughtlessly tells them that Chrysalis claimed they were in the wedding only because they wanted to meet royalty. Offended that anypony believed such slander about her, Twinkleshine bursts into tears as the crowd's ire toward Shining Armor grows.Shining Armor: I didn't mean to hurt her feelings!
Twilight: But you did! Just like me.
- Suddenly an egg is thrown in the silent Celestia's face. The thrower turns out to be a filly who tearfully tells that her parents were attacked by Changelings and are still in the hospital, blaming Celestia for it. A random mare then screams that her husband, a member of the Royal Guard, died. Celestia says nothing but feels pity and guilt.
- When Celestia is given a chance for final words, she sadly apologizes to Twilight and everypony else for failing them and everypony who lost their lives, accepting that perhaps she's not meant to be Equestria's princess anymore. She believes that she could have prevented all the suffering caused by Jewelius had she not placed her trust in the wrong ponies. As a last token of love and caring, she raises the sun and asks Twilight to take care of everypony for her. Twilight and the crowd are so moved by Celestia's remorse that they start demanding Jewelius to stop the execution. They're unable to change his mind and watch in horror as Celestia falls through the trapdoor. Fortunately, Luna saves her sister.
- Lyra Heartstrings, Minuette, and Twinkleshine call the heroes out for not caring about their disappearance and the Mane Five of shamelessly replacing them as bridesmaids. Shining Armor thoughtlessly tells them that Chrysalis claimed they were in the wedding only because they wanted to meet royalty. Offended that anypony believed such slander about her, Twinkleshine bursts into tears as the crowd's ire toward Shining Armor grows.
- When the fugitives go seek shelter from Ponyville, it's revealed that Jewelius has been persecuting the entire town with raised taxes and trading prohibitions because it's the home town of the "traitorous" Mane Five. Nopony dares to walk in the streets anymore because Jewelius' soldiers might come to punish anypony who tries to go against the harsh laws, or cause trouble just for laughs. Mayor Mare offers a hiding place in the town hall for ponies who resort to thievery in order to provide for the needy (one of the hiders is Scootaloo), the Cakes have barely enough food to feed themselves and their twins, and the Apples have been forced to harvest about all their apples without having the time to grow more for the starving ponies.
- The moment Twilight finally realizes how evil Jewelius — her new friend, mentor and fiancé — truly is. After he has forced her into submission by threatening the lives of her imprisoned parents, and she's left alone in the throne room, she breaks down, feeling the same sense of loneliness and betrayal like she did when she was abandoned at the rehearsal, with the added guilt over treating her former loved ones the same way they treated her back then. Fortunately, Raven Inkwell (who is actually a Changeling in disguise) arrives to get Twilight out of this predicament by freeing her parents and helping them escape.
- At the beginning of the 17th chapter, the Mane Five and Spike are on the verge of losing hope when they are unable to come up with a plan to stop Jewelius without Twilight, admitting that the villain was right about them being nothing without her.
- The 17th chapter's reconciliation moment between Twilight and Shining Armor. She begins by blaming herself alone over everything that's happened between them, tearfully saying that she'll do everything in her power to earn his forgiveness. Unable to just listen and let his sister take all the blame for herself, Shining Armor sheds more tears than her while speaking and tries to take all of the blame instead.Shining Armor: How can you say all that?
Shining Armor: How can you put all this blame on yourself when most of it wasn't entirely your fault? How can you still call me that? How can you still love me after what I did?
Twilight: You're my brother, I will always love you no matter what.
Shining Armor: But you were right. You saw the signs, you tried to warn everypony, we didn't listen, but you were right. I made you look like such a horrible person in front of everypony. I kicked you out of the wedding that you set into motion a long time ago. I should've followed my instincts like you did. I should've known something was wrong with the bride. I should've listened to you and I'm sorry. I am so sorry.
Twilight: Please, no more. [hugs her brother who reciprocates in kind, with Cadance also joining in]
- Though Lieutenant Shackle undergoes a HeelFace Turn and helps the heroes win the final battle, she is so wracked with guilt that she chooses to go to prison with the other conspirators and be a better pony after her sentence is served.
- Despite everything Jewelius had done and his well-deserved end, the heroes especially the three princesses are saddened that he couldn't have been redeemed. He may have been evil, but he was still the princesses' family.