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- Miranda risking her own life and career to bail Alex out of FBI custody at the end of "Pilot".
- Simon assisting Alex to clear her name despite his potential FBI career being ruined when he got the boot in "Cover".
- While the FBI agents tear each other apart in their psychological reports in "Cover," what does Caleb have to say about Shelby? A single word: "Nice."
- Miranda talks about her son being radicalized into a terrorist. It broke her heart that he had to be arrested.
- Miranda talks to Alex and comforts her that she did the right choice in shooting her abusive father since he had a bad reputation in the bureau despite his good record.
- Caleb helping Raina through the training exercise in "Kill".
- Booth, Shelby, Simon and Alex willing to help Raina get to Nimah in "Go", especially as both Simon and Nimah flat out refused to go anywhere without her.
- Back in their Quantico days, Miranda introduces the Amin twins to the other recruits who are still in the academy.
- In "Clear", Natalie gets a suicide belt strapped to her, and she and Alex spend a hellish day being blackmailed by the Big Bad into pulling off a data theft that they by all rights shouldn't be able to accomplish. Despite the odds, these two former rivals work together to steal and deliver the data and Natalie's belt is disabled, and she and Alex embrace each other. The relief that they share is palpable.
- Raina's phone call with Simon where she confides in him about not knowing whether or not she should lie about Miranda's involvement in her infiltration of a terror cell. His attempt to make her feel better and reference to the fact that they had spent New Years together were very sweet.
- Raina's willingness to do whatever it takes to help Alex and her other friends, even if it means breaking the law and opposing her own sister.
- Alex, Shelby, Caleb and Will all being on good terms again in the present.
- Lydia's explanation of why she's hard on Alex in Lipstick.
- Nimah being the one to recite the Mourner's Kaddish while she, Alex, Shelby, and Ryan visit Simon's grave in Aquiline is a cross between this and a Tear Jerker. After how antagonistic their relationship was for the majority of season one, and how earlier in the same episode, Nimah had said that Raina saw her as a reminder of the pain of losing Simon, it came across very much like an apology for how she'd treated him.
- Shelby and Nimah's relationship throughout the whole season has its ups and downs, but the deep affection they have for each other, even when Shelby is upset at and angry with Nimah, is constant.
- In Mockingbird, Nimah really finds her place on the team, with Shelby telling her that she absolutely belongs and Clay apologizing for the way he treated her.
- Also, as the team heads out to the bar, Ryan puts his arm around her and she steps closer to him. It's very touching to see Nimah, who is often emotionally distant from the rest of the team as well as the one who has the least physical contact with others, display affection for others and have them respond.
- In MKTOPAZ:
- Shelby calls Haifaa and tells her that it's good to see her.
- Shelby tells Clay's fiancée that he was the one his family got right.
- Ryan and Alex both tell Nimah to call Raina.
- Ryan telling her to call was especially sweet because in season one, he gave Raina similar advice about finding an emotional anchor.
- Nimah taking Raina's place and turning herself in after Raina is framed for a bombing.
- Alex, Owen and even Ryan use ASL at least on occasion with Jocelyn, who uses it as her prime mode of communication.
- In "Spy Games", Prince Khaled's father dies and he is expected to become the new Emir of Qumar, and has only one night left before taking the throne. How does he choose to spend it? By making dinner for Alex and McQuigg in order to thank them for protecting him.