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Back from the Dead - Stef, once as a child, and then again when she's stabbed by a piece of mirror at the end of Mirrorfall. It also happens throughout the later series as Agents have a 're-spawn' function and the mirror refuses to let Stef stay dead. Taylor is also an example.
Playful Hacker - how Stef makes her living before joining the Agency. Also, arguably the entire tech department.
Cold-Blooded Torture - A reoccurring theme in the series. Details are not spared. We see the effects of it on the characters Stef many many times, but also what causes people to do it Curt is a reformed Torturer/Interigator
Deadpan Snarker - Curt is certainly one. Very good at impromptu snarky lines.
Primarily with the Ryan/Stef dynamic (developed through MH, stated openly in MS, now he routinely refers to her as his daughter).
Jones for Merlin.
Agent Mike and his adopted son Bennefree.
Agent "Billy" Williams and Milla.
Freak Out - Stef, several times, most noticeably in MH where after being shot the first time after coming back she descends into a full meltdown, externalising the voices in her head, quoting River Tam and playing with small pieces of her own brain.
Stef's were emotionally distant and sometimes outright neglectful - prime example being they failed to notice the events of MF#01.
Her father goes beyond emotionally distant and neglectful when he shoots her in the head in the fourth book Oubliette
Small Girl, Big Gun Subverted. Stef is asked to pick a gun and chooses a sensibly small "girly gun". Ryan even comments on how every recruit picks out something unsuitably large like a desert eagle, to which Stef responds "‘I think,’ she said as she handed the Desert Eagle back, ‘I’d break my damn nose if I tried to use that thing.’"
Merlin's parents...as of book four, only hints have been dropped, but the consensus is "Oh boy..."
Split Personality - Stef hears a voice in her head (which fans refer to as Boldvoice). She generally known of as the sensible one who keeps them both alive. When Ryan goes into her mind he meets a two of Stef, supporting the split personalty theory for Boldvoice. Generally Boldvoice cannot control Stef but has spoken through Stef and even performed actions specifically during her attempted suicide in Obilette