Dalek Sec: I RE-FUSE TO GI-VE UP AND RE-DUCE MY-SELF TO U-SING "MA-GIC" AS AN EX-PLA-NA-TION FOR E-VERY-THING. THIS IS SCI-ENCE, WHERE A IS E-QUAL TO A, CA-USE HAS EF-FECT AND THI-NGS DO NOT HAP-PEN "BE-CAUSE SO".
Badass: Sec. Note what happens when he deals with Familiars.
Badass Pacifist: Madoka, who convinces Sec not to crush Kyoko's skull during their first encounter with her. When you can talk an Omnicidal Maniac out of killing someone, there really isn't anything else you could possibly be but this.
Bad Boss: Sec's former commander, The Dalek Inquisitor General. To the point that he got promoted to Supreme simply by virtue of surviving five consecutive missions under his command.
See below for a perfect example in Who Wants to Live Forever?. Madoka thinks that immortality is a curse after hearing Homura talk about it. Sec, on the other hand, is proud to have lived to be a quarter of a million years old.
Cassandra Truth: "I AM AN IM-PERIAL-ISTIC SPACE NAZI." Though played with in that he says that he deliberately tells the truth because it's so ridiculous that everyone just forms their own conclusions anyway.
Character Focus: Read this page. Notice how someone keeps getting mentioned.
Word Of God has it that this is to make up for the fact that he wants to make a believable and interesting character out of something that usually isn't.
He has also stated that he'd like to get more PMM characters and elements in on the action, with a little less focus on the Doctor Who side of the crossover.
Continuity Nod: Given the events of Satellite Five where it's revealed that the Dalek Emperor has been doing pretty much exactly what Kyubey has in this story, you'd be surprised at the attitude that Sec takes towards Kyubey's cultural manipulation of humanity to be more pliant. However, if you remember "Daleks In Manhattan," the human spirit and their capacity for endurance, rebuilding, and survival against all odds were things that Sec very much admired, calling it "Almost Dalek." It makes sense that he hates Kyubey...
Cosmic Plaything: Dalek Sec is absolutely convinced that the universe (or at least some god-like entity) is actively screwing with him. He isn't happy about it. Atall.
Crack Fic: Played with. The general idea of the fic, that a Dalek would turn into a hero, is very, very crack-y. The rest of the fic isn't.
Homura: There was nothing there that could've caught fire, there was nothing there to spark a fire, and there was absolutely no reason at all for a Grief Seed to catch fire.
Homura: Then why did that thing catch fire?
Sec attempts to play Dwarf Fortress and somehow manages to trash 69 fortresses in a few minutes.
Even Evil Has Standards: Played with. Sec's human morals tell him that what the Incubators are doing is wrong even though as a Dalek, he approves intellectually of the concept behind their operation. What he doesn't approve of is the Incubators undermining the human race's right to self-determination by manipulating their cultural and social evolution to make them more pliable and easy to manipulate.
Also, Sec's opinion that it would be cruel to put anything inside the improvised Dalek shell he constructs in chapter 2.
Exact Words: Kyubey, but that's nothing new. Sec also mentions to Madoka that Walpurgisnacht will devastate "The Area." What she hears is "Destroy the city." What he means is "Annihilate the entire star system".
Flat "What.": Homura gives one when she realizes that even though she's severed the link between her soul gem and her body, and is effectively deaf, she can still hear Sec ranting.
Fluffy the Terrible: Kyubey, as in the main series. The difference is that from the beginning, we know he's one of these instead of being the standard Magical Girl mascot. Also, while he/it tries to use Cuteness Proximity to appeal to human females, it fails hard against Sec.
For Want of a Nail: Besides the obvious, Sec's presence has changed a lot of the storyline.
For example: the conversation between Madoka and Homura in chapter 4, which has Homura revealing to Madoka that Puella Magi do not age. This causes Madoka to later figure out part of the reason why Homura is so insistent in not having her contract with Kyubey, as well as giving much Fridge Horror for the poor girl.
"Groundhog Day" Loop: Still very much in effect here. Homura's not getting out of this thing any time soon.
The Doctor's here now, as well.
Hold Your Hippogriffs: Dalek Sec, being a non-human, has a few of these. His main one is "SON-OF-A-THAL!"
Humanity Is Infectious: Zig-zagged all over the place. On one hand, Dalek Sec now has human emotions. However, it's because of his attempt at hybridization in "Daleks in Manhattan," but he's also trying to work through those feelings. And while he's trying to examine human culture... it doesn't always go quite as simply as some of the more iconic examples of this trope. See also, Dwarf Fortress or his reaction to Avatar. But on the other other hand, he views humans as a great species because Humans Are Warriors. See below for more clarification.
Omniscient Morality License: The Incubators, who have not only been exploiting the human race since the stone age but have also been conducting social engineering projects to make humans easier to manipulate. Sec implies that they're responsible for creating the cultural image of the Magical Girl which misleads so many young girls into contracting with them.
Reality Warper:Sec inadvertently warps space-time by projecting a block-transfer equation onto a wall, which is hovering above the wall even after the projector is turned off.
Really 700 Years Old: There's no indication as to how many times Homura's repeated the "Groundhog Day" Loop, but she's done it enough times to memorize nearly every single event in Mitakihara that could be remotely relevant to her cause, and learn nearly every single possible route in which events could unfold.
Sec claims to be 250,000 years old.
Refuge in Audacity: Sec's strategy for remaining inconspicuous is to advertise the fact that he's an alien super-Nazi at every opportunity. Naturally, nobody believes him, and they come to their own conclusions.
Running Gag: Sec never succeeds in his first attempt. Or in his second. Or third. And yes, this applies to everything, up to and including video games.
Unexplained Recovery: Sec, obviously. Absolutely no indication of how he managed to survive is given, or how he managed to get his casing back, or how his previous condition was negated. Lampshaded at once, with Sec promptly deciding that he doesn't want to know how he managed to survive.
In chapter four, the Doctor claims that when Amy rebooted the universe at the end of series five, it accidentally brought back everything that had ever died. Most of it died again, like it did in the original timeline, but Sec was somehow thrust into the Void, where he eventually wound up in the PMM universe. Word Of God states that the reason why the Doctor and Sec were able to get to the PMM universe is because someone came here during the first time war.
Dalek Sec wasn’t quite near the I-will-kill-everyone-on-this-planet-with-their-own-internal-organs stage yet, but he was certainly getting there.
Noted slightly earlier that what a human considers "Unstoppable Rage," is merely "Miffed," to a Dalek. If any other life form in existence felt what a Dalek considers unstoppable rage, they would explode.
Subverted with Sec, and the subversion is justified: increased age means more combat experience, so having survived a very long time is a badge of honor for him. Also, he wants to restore his race eventually, and given his first attempts to create Dalek Embryos (in Daleks in Manhattan) and his first attempt at making a casing (chapter two of this story), he's probably gonna be around for a while.