The scene at the end where Reverend Mother sternly defends Deloris as a nun and "a model of generosity, virtue, and love," in spite of it being Blatant Lies, which shows she cares for Deloris so much that she will even break one of the Ten Commandments just to save Deloris from being killed.
It's possible that she isn't lying since Deloris, after a rough introduction, did go on to prove herself to be a loyal friend to the nuns, befriending many of them and using her talents to improve the convent with no thought of reward other than a desire to help the sisters. That covers generosity and love, at least.
When Deloris realizes that for all her stern, gruff ways, that she genuinely cares about the other nuns and she responds, "Yes. And I care about you and your life."
She proves this with her genuinely terrified "Oh, my goodness" when Lt. Souther tells her that Vince knows where Deloris is.
"Out of bed, you Daisy head." That whole scene with Mary Robert, actually.
The scene after the first choir practice, when Deloris is lying in bed listening to all the nuns practicing their chords, and it ends with Mary Robert hitting a perfect, beautiful note. The smile on Deloris's face really sells it.
The look of pure joy on Mary Robert's face after her first solo during "Hail Holy Queen."
Which leads to another heartwarming moment when you can tell she has immense confidence in her voice during her other solos. (And then immediately afterward she's blushing and trying to cover her face, like 'What did I just do?')
Mary Robert's joy here isn't entirely because of her newfound confidence; with Deloris's help, she has discovered a talent that will help her to better serve her faith and her god, which is the reason she has become a nun in the first place.
Well, heck, every scene with Mary Robert is Heartwarming.
Also, look closely after Mary Robert's solo in "Hail Holy Queen." As she turns in thrilled excitement, Sister Mary Lazarus has a huge smile on her face and congratulates her on a job well done.
The Hail Holy Queen song has a number of thoughtful touches throughout, even in the background. All of the singers look extremely enthusiastic and joyful while performing, clearly having taken Deloris's early lesson of "...it's not just quacking, this is rejoicing." to heart. Shots showing the congregation in the background show a number of people swaying, clapping or otherwise getting into the rhythm (one brief shot shows a character very enthusiastically swinging their arms to the music). The response to the new upbeat presentation from the choir is evident even before the applause at the end.
During the singing of "Hail Holy Queen," a group of delinquent teens enter the church, attracted by the music. As soon as the monsignor notices them, he waves for them to come inside, nodding his approval.
Those same teens are seen in the second row of the Pope's concert, behind the monsignor and Lt. Souther, implying they have become regular congregants.
The two altar boys swinging their legs, and smiling at each other. Good to see them enjoying it too, and unlike a lot of things in the film that stretch the audience's beliefs, this scene is 100% believable.
In universe, how the nuns feel after going out into the community after being cloistered for so long. They long to do good works and now they finally get the chance to revitalize their run-down neighborhood.
It works as an audience example, too. We see the nuns going into the community; rather than proselytizing, they strike up friendly conversations, run a soup kitchen and garden market for the homeless, create beautiful artwork out of ugly graffiti, and fashion a playground for poor youth out of junk. Deloris even leads Sisters Mary Patrick and Robert in meeting some teenagers, and the two groups create a genuinely friendly bond over jump roping and dancing. Even atheist YouTube users comment that the spirit of the scene—that of religion doing small, good deeds with compassion and producing tangible results for those in need—is a powerful, positive one.
During the kidnapping, Joey and Willy also get their hands on Sister Mary Robert. Deloris manages to get her out of the car and convinces the two men that she's not worth chasing down.
After Joey and Willy grab Deloris, the rest of the nuns express confusion as to why anyone would kidnap a nun, so Reverend Mother decides it's the perfect time to come clean about who "Sister Mary Clarence" really is. While the nuns are obviously stunned to learn that she's a lounge singer who was placed in the Witness Protection Program after witnessing a murder (as well a little upset about being lied to), Sister Mary Robert declares that she doesn't care who Deloris really is—actual nun or not, she saved the church and the choir, and that's enough to make her a loyal friend and a good person. Sister Mary Patrick supports this statement, then Sister Mary Lazarus says that they shouldn't leave saving Deloris up to the feds if they can help it. The rest of the nuns, including Reverend Mother, agree and they immediately set out to Reno.
Then after Lt. Souther manages to arrest Vince and his goons, they reveal to Deloris that they know her true identity and are pretty good natured about it.
At one point, Sisters Mary Robert, Patrick, and Lazarus sneak Deloris down to the kitchen at midnight and produce some "contraband" for a secret snack...tubs of ice cream. Even Mary Lazarus, who first calls it a "wicked indulgence," wants to know where the butter pecan is. It's small and even silly, but seeing the nuns so happy and thankful to Deloris that they're willing to bend their vows is adorable.
From the same scene, Mary Robert reveals that she thanked God in her morning prayers for bringing Mary Clarence to the convent.
During the first rehearsal scene, Deloris takes over the choir. At first, she's reluctant, but as she gradually gets into the role, she rearranges the room and demonstrates her strong knowledge of music. She even gets into the spirit (literally!) of the convent by pointing out that singing is a form of praise and worship. It's the first time we see her genuinely beginning to enjoy herself and relax, and makes it clear that there's a heart of gold beneath her snark.
From the same scene: Mary Lazarus was the former choirmistress, and though she's at first sarcastic, it's soon apparent that losing the job has hurt her. When she claims that she has music knowledge too ("I knew that..."), Deloris realizes that she's feeling bad and finds a way to keep her involved as a leader, asking her for advice and allowing her to make the rehearsal schedule. Mary Lazarus is thrilled to help (not that she'd ever admit it), and again, it shows the kind side that the convent reveals in Deloris.
And in their first song as a group after Deloris takes over, Deloris has fully integrated Mary Lazarus, even giving her minor solo bits. It's heartwarming to see how much she and the rest of the choir are having so much fun performing.
The finale. Earlier in the movie the Reverend Mother and Deloris disagreed on whether to sing a traditional performance or one of Deloris' more upbeat versions for the concert with the Pope, with the RM eventually losing when they put it to a vote with the other nuns. When the time finally comes, Deloris leads the choir in a traditional song first, before switching to her style.
Note the reversal; the choir started out by jazzing up a traditional hymn, but now it's a secular song that gets the traditional treatment, showing the Reverend Mother's influence on Deloris.
Just before this, we have the Reverend Mother and Deloris' reconciliation. Not only is there her Arson, Murder, and Lifesaving bit followed by a sincere thank you, but they share a hug (after Vince almost shoots Deloris, both women are shaky and seem to need it). Then she declares they have to get back to San Francisco for the concert. When Deloris questions her on this, both for her change of attitude and the fact she had planned to resign, she turns and smiles, confiding to Deloris alone, "We can't both of us leave."
The Second Movie
Deloris has very little hesitation when she hears about how much the nuns need her help and that Mother Superior is "desperate".
Both Deloris and Mother Superior get huge smiles upon their reunion.
In Deloris' big stage show, she still has Tina and Michelle as backup singers.
Rita's mother finally approves of her singing after hearing her shine at the competition.
Deloris saves the day by winning the competition, and having the kids sing a hip-hop version of a classic hymn. Not only does this showcase the children's natural talent and their own particular style, but it saves the school from being closed and turned into a parking lot.
The Musical
Deloris hands Mary Robert her thigh-high boots "if you feel you need a little adventure in your life." Even better, she wears them during the Pope show.
Eddie praising Deloris on her many talents, even saying that in high school he always knew she would be famous.
The title song is a What You Are in the Dark moment for Deloris. She starts off singing about how she could continue her career without worrying about the nuns, but then she realizes how much her sisters mean to her and decides to help them rehearse before the Pope concert.
Deloris's relationship with Mother Superior by the end. They have clashing beliefs, but then Mother Superior realizes that faith is both God and human, then states that they are one in the same. Deloris gives her a big hug in response. Even though Deloris doesn't believe in praying, she concludes that it gave her a true connection to everyone in the convent.
