A lot of what has happened in My Brave Pony: Starfleet Magic is brought up again, only with a more sinister context behind them in Fall of Starfleet, Rebirth of Friendship.
- The Equestrian population apparently blacked out during the formation of United Equestria and were horrified at their new anatomies when they woke up.
- Starfleet arresting people who so much as disagree with Grand Ruler leads to many said prisoners joining Dark Conquest to get their revenge.
- Starfleet tampering with Ace Ray's mind has left him in a coma-like state. Though he manages to recover.
- The Flanderization of the Equestrian cast was due to Grand Ruler manipulating their memories.
- On a similar note, this applies to practically all of Starfleet's adventures as Grand Ruler was manipulating everybody's memories to make Starfleet look more superior and heroic.
- Celestia marrying Celesto and Fluttershy marrying Rhymey was due to the Unicornicopians manipulating their minds.
- Starfleet relying solely on their memory scanners and their faulty justice system, in general, has led to countless innocents being thrown in jail.
- In Starfleet Magic, Daphne Dil mocked the very concept of a cutie mark, saying that even if she could get one, she wouldn't want one. In Fall of Starfleet, Daphne is jealous and upset over not being able to get a cutie mark because of how they can tell a pony what they will do later in life.
- Lightning Dawn (unknowingly) had a hand in Twilight's death when he disabled her magic while she was fighting Raven. Understandably, he is shocked about this.
- Raven's hatred of Celestia and her current status as an Ax-Crazy Blood Knight comes from Dr. Emil Kudos and Grand Ruler experimenting on her. By extension, basically everything about Emil Kudos gets this treatment.
- The rare golden horns in the series do not occur naturally, and are in fact an extension of Celesto's power. They also serve as a Restraining Bolt of sorts by modifying the bearer's memories, most of which can be unlocked by removing it. Additionally, they serve to amplify his mind control powers and spread it among those around the bearers.
- In "The Fall Ends, Pt. 2," Grand Ruler's golden wings are revealed to be fake and mechanical, placed onto himself with the Orb of Reality to further bloat his own ego when he arrived onto Unicornicopia. Two of his three horns are also fake, and his real one slotted into the Tri-Horn Crown, which itself is destroyed by Conquest during their battle.
- Grand Ruler didn't create the Unicornicopians, either, nor is he himself a Unicornicopian. Conquest reveals to United Equestria that he, in fact, discovered them when he was banished to Unicornicopia after Luna became Nightmare Moon and blasted him with a spell, then proceeded to subjugate and brainwash them. And that 'Grand Celestial Ruler' fusion never, ever happened either; Celestia and Luna dealt with Titan when the supposed fusion took place. Grand Ruler merely twisted events about that too, if only to further stroke his ego.
- In "The Fall Ends, Pt. 2," Grand Ruler's golden wings are revealed to be fake and mechanical, placed onto himself with the Orb of Reality to further bloat his own ego when he arrived onto Unicornicopia. Two of his three horns are also fake, and his real one slotted into the Tri-Horn Crown, which itself is destroyed by Conquest during their battle.
- Lightning's hometown was destroyed and his family killed by Rhymey, under Grand Ruler's orders, so Lightning could have a tragic background befitting the hero of Starfleet. Something similar happened to Cerise.
- Serpent Tyrant/Serpentari is a Starfleet-based Doomsday Device rather than a monster; the latter is a cover story fabricated by Grand Ruler.
- Chapter 16 reveals that the Dark King and his minions (Giant, Demon, Ogre, Alien, and Bad Horse) are respectively, the Bad Future counterparts of Shining Armor, Big MacIntosh, Pound Cake, Zephyr Breeze, Sweetie Belle, and Soarin. The future they all come from is one where Cadance had a miscarriage, while the remaining Mane Six continued drifting apart and ultimately all ended up dying, mostly from suicide. Cadance and her artificial second baby died soon after, which led to Shining Armor falling over the Despair Event Horizon and becoming hellbent on destroying Grand Ruler.
- Bad Horse/Soarin lost his wife Spitfire and their child to Starfleet's carelessness and joined the Dark King's ranks to avenge them. Presumably, all of the others had similar motivations, given the deaths of their own loved ones.
- Chapter 17 reveals that Lightning Dawn's enticorn form is a corruption of an ascended Alicorn form powered by hatred and rage.
- Why the Space Ponies are superior to other species at certain times yet at other times tend to be outclassed by those same species is explained as them possessing innate magic that improves their strength, speed, or intellect in times of danger, but cannot be accessed voluntarily.
- Melantha, one of Sombra's generic underlings in Starfleet Magic, is retconned into a Serial Killer.
Evolution Of Friendship
- It seems Mystic Island (where the Starfleet Humans series takes place) spontaneously appeared on Earth from out of nowhere.
- The people who bullied Human Starla in the first Starfleet Humans story was actually coerced into doing so by Starla herself so that Lightning would save her.
- Characters are wondering how Celesto Grandruler went from being a farmhand to a millionaire astronaut. Sunset Shimmer is even investigating him. The truth is not pretty.
