Even in the midst of being abruptly transported into this bizarre other universe, and given a ridiculously small amount of time to prepare, Phoenix still takes the case, as it would go against all his principles to turn it down.
Twilight's relieved reaction when Phoenix tells her he'll take the case. She explains that had he refused, she would have studied law books (likely all night) so she could represent Rainbow Dash herself. In other words, she fully intended to return Phoenix to his world had he not been willing to represent her friend, when she could simply force him to by refusing to send him back.
Phoenix reminiscing about him once being accused of murder and telling Twilight how he was inspired to become a defense attorney. He mentions finding strength and support from one's friends even in the darkest of times, an idea that is at the very core of the MLP: Friendship is Magic series. Twilight herself seems quite moved by his story.
This point gets driven home when Phoenix is still determined on getting Rainbow Dash acquitted, or helping on doing it, even after knowing that Twilight was planning on firing him; he just can't allow himself to let the innocent be punished. Twilight is very surprised to hear this, and it no doubt plays into her decision to forgive him.
Dash is really harsh against Phoenix for his "terri-bad" performance in the first day of the trial. A bit later Phoenix manages to see through her lies and break her psyche-locks, which makes Rainbow stop her harshness and respond with sincere respect towards him, something quite rare from her.
The Judge's excitement about exploring Equestria after the trial, and assuring Twilight he was just doing his job in siding with Trixie's sounder objections.
Cruise Control tells Twilight what he has been forced to do thanks to Ace Swift's blackmailing, and laments about his sister, saying that he doubts that she'd look up to him the same way as she did before. Twilight tells him that she'd look up to him even more; he's willing to hold back on something he loves for her sake. He has a clear change of expression when she says this.
Twilight:I think you're a good big brother.
The impact of this part increases when you realize that Twilight would know because she has an older brother. Though when you take into consideration that the story was written before Season 2, it becomes all the more sweeter since it's Heartwarming in Hindsight.
When Twilight manages to break the final psyche-lock without drawing on any evidence, Cruise Control outright thanks her for figuring it out on her own.
Twilight wants to run out to find Fluttershy, but there's the little problem with the trial about to take place.
Phoenix: Ugh... As Rainbow's "out of town" attorney, I really wouldn't recomend you leaving me alone in there... Twilight: ... Phoenix: But, as your friend, I understand.
After that, he tells she shouldn't worry, since he spent the last night doing some studying on his own. After a pause, she makes the most relieved and sweet of smiles.
Fluttershy arriving to be the Big Damn Hero despite the scathing "never want to see you again" What the Hell, Hero? that Rainbow Dash had delivered earlier. Furthermore, her additional testimony is based on evidence that Phoenix uses in the latter part of the session, meaning that she returned much earlier and had been watching the remaining trial.
Phoenix shows the extent of his ideals when he stops the Judge from handing down an easy Not Guilty verdict after Sonata's confession to prove that she's not the murderer. In essence, the final confrontation is changed from its usual function as the final nail in the coffin for the guilty party, and instead becomes the light of hope Sonata needed so much.
Sonata: Why would I lie confessing my guilt? I suppose if I was trying to protect someone... Trust me, that's not the case. Because the sad truth is... I don't have anyone to protect. Phoenix: Then let me protect you.
Yet another case of Heartwarming in Hindsight, though this time for Phoenix's series. Turnabout Reclaimed ends the exact same way.
Sonata taking the first steps to repent for all she's done by donating Ace's entire fortune to Cruise Control's sister's medical case, in addition to ensuring once and for all that she stays in the hospital she needs. She even entrusts Twilight with carrying it out, due to her impending incarceration, and asks Phoenix to tell Pinkie that her odd grimaces were actually efforts to hold back laughter. Really, her entire Heel–Face Turn is a long heartwarming moment, especially from the instant she takes off her glasses (not actually needing them) and genuinely smiles as she thanks Phoenix for giving her a second chance.
After the trial, Fluttershy's whole speech to Rainbow Dash about why she stuck around during the trial and why she got back up on the stand, ultimately ending in the two of them making up. It manages to bring Rainbow Dash to tears, though she denies it.
This is followed by Twilight's friendship report on the events, which she makes Phoenix proofread. "Friendship IS unnecessary... Like art, poetry and music. We don't need it to survive like food and water; rather, it's one of those things that gives our life, and other lives, value and meaning. (...)". The fact that these scenes are accompained by Turnabout Sisters Ballad doesn't hurt in the slightest.
Phoenix: ... It's perfect.
The moment every Lyra fan has been waiting for since the series began: She meets a human!
During the credits, we learn that the Equestrian 500 was called off due to everything that had happened. Regardless, Rainbow Dash, Lenora, and Cruise Control decide to hold their own race since Rainbow Dash lost out on her chance to compete. Especially heartwarming is seeing Cruise Control finally at peace now that Sonata is using Ace's fortune to fund his sister's treatment and ready to give it his all.
Twilight's final goodbyes to Phoenix, including her sadness at not being able to share more time with him outside of investigation, and her reassurement that, no matter how far they might be from each other, they'll still be friends.
Twilight: Anyone who ends up with you as a lawyer is really lucky. No... anyone who ends up with you as a friend is really lucky. Let's keep it that way.
At the very end of it all, Trixie secretly sends Phoenix home with a blue silk magician's hat after hearing him admit to wanting one as a kid. The fact that it looks almost identical to the top hat Phoenix's adoptive daughter Trucy would come to wear in later years only makes it better — for all we know, it might be the same hat.
In addition, inside the hat is the picture they all took together, with the words "Thank you." written on it — and Trixie's cutie mark as a signature. Despite her condescending bravado, she actually is grateful to him for proving her wrong and setting her on the road to rebuilding.
Phoenix:You know... maybe I did get something out of this after all...
The final stinger has some sweet moments made clear after the cryptic part of the conversation is figured out. Mia is very proud of Phoenix, and seems to be in friendly terms with Celestia despite the short time she's known her.
Not to mention: According to Mia, Equestria bears a remarkable resemblance to Heaven.
In real life: The 9 year old girl who voices Apple Bloom told NeoArtimus that she wanted to leave after some nasty comments about her acting; this forced her to hold auditions for a new actress. After learning the actress' motive, many fans sent her supportive messages, but she was still dead-set on not coming back. Then Michelle Creber, Apple Bloom's actual voice actress in the show, sent her a supporting message, ultimately convincing her to stay with the project.