and I didn’t take any notes. So, either I was too tired to spot any errors, or all the nitpicking is already done :-)

I liked Nicky’s reaction to being in a live action world. Not knowing her home continuum, I had never realized that she is a big-eyed anime character.

Apparently something more sinister than Mary Sues is at work here. Are “they” the maleficent force behind the Mary Sue factories, or did “they” just buy a special offer of Defectives to do the dirty work? Going off topic (or maybe not?) I never quite understood the economic reasoning for Mary Sue factories. Do they sell Mary Sues to writers who are too lazy to make up their own original character? Or do the factories create all these Mary Sues just for the fun of being evil?

I’m looking forward to the next chapter.

HG

"None of the windows was facing towards the two Agents" That should be "were", not "was", since there had been multiple windows.

"[I can’t open the portal directly from the console, either,] Corolla added, [I’m afraid there’s a plothole near you.]" The comma after "added" should be a period.

"Ben, do you think we’re going to get back the car still in one piece?" The words "the" and "back" should be switched, and the word "still" may not be needed. It's not grammatically incorrect to include it, but it's a little awkward.

"it’s the tech that isn’t working. Also, calling a taxi would’ve took more time," Again, not strictly grammatically incorrect, but swapping "that" and "tech" would make the phrasing a little less awkward. What is grammatically incorrect is the use of "took" instead of "taken", though I'll admit the misuse of "took" does occasionally occur in spoken English. Sergio hasn't shown proclivity to use dialect, though, so I'm pretty sure it's just a grammar mixup.

"we’re on an highway," That should be "a highway".

"changed lane to let a Porsche go past, “see? He’s doing at least two hundred," There should be a period after "past", not a comma, and "see" should be capitalized.

"A different art style doesn’t change who you are, though," Sergio said, "or who I am, for that matters." The last word should be "matter", unless the meaning would be synonymous with "because that matters", which would be a bit strange in that sentence.

“I would’ve asked to the dock workers, but this place looks pretty empty,” That should either be "asked" or "talked to".

"Sergio explained, “besides, the container was to be loaded today," "Explained" should be followed by a period, and "besides" should be capitalized.

“I think I have an idea,” Nikki said, “the CAD should be able to find Madoka and Sakura". "Said" should be followed by a period, and "the" should be capitalized.

“I hope this isn’t going to become another six-”
[Bestest Shipping Co. container holding character Madoka Kaname. Uncanon. Suggested action: Open container and liberate the canon character.]
“Sometimes I have the weird feeling these things are mocking me,” Nikki deadpanned.
“Only sometimes?” Sergio asked while stopping the car next to a black container, “this one?” Other than the period-capitalization replacement again(for "container," and "this" this time), I think there might be a step missing here, unless Nikki's CAD states its readings out loud, and even then it's a bit of an issue. Nikki is about to say "six-hour search", sees the reading, stops after "six" because she sees the CAD readout, and then Sergio suddenly knows which crate has Madoka in it? If it was just a readout, she'd need to tell him and indicate which crate the CAD had been scanning when the readout came up, and if it was read out loud, which is atypical and a little impractical for CADs but within the realm of possibility, she'd at least need to nudge him and point or something. Sergio's shown no signs of being telepathic, and the readout didn't exactly say specifics to the level of "in the little brownish-gray one, second from the left of the north wall" that would have led him to just be able to pick it out.

"Yes. Let’s get her out, I don’t think it’s very comfortable in there." That should be two sentences, divided by what is currently a comma. If you would prefer it stay in one sentence, you can substitute with a semicolon. There's another comma splice at "We were lucky, ours is on the ground," which can be fixed by either making that into two short sentences or rewording the phrase as "We're lucky that ours is on the ground." Using a semicolon in that case would create a mid-sentence tense confusion.

"Sergio muttered as he inspected the padlock keeping the container locked." A little redundancy here. A suggested rephrase might be "Sergio muttered as he inspected the container's securely fastened padlock." I was going to say "sealed padlock" to spare a word and keep a little more ambiguity, but I'm not sure if closing a lock can be referred to as "sealing" it.

"[Hm, I wonder where Sakura is.]" This should be "[Hm. I wonder where Sakura is?]", since periods at the end of questions tend to usually evoke disinterest or at the least a flat tone of voice.

"I know who you are,” Madoka interrupted him, “you’re Sergio Turbo and Nikki Cherryflower from the PPC, right?" Capitalize "You're", and replace the comma after "him" with a period.

"Sergio continued, “until we catch the one who kidnapped you and Sakura" Capitalize "until", and replace the comma after "continued" with a period.

"Corolla confirmed, [I'm afraid" That comma should be replaced with a period.

Sergio said, "In the meanwhile" Comma-period switch again, and you should replace the word "meanwhile" with "meantime". Alternatively, you could delete "In the" and just leave the "Meanwhile", but that doesn't work quite as well in this context.

"Nikki agreed, “If they" Comma-period switch again

"Both of you,” Madoka said" Comma-period switch again.

"… We are being shipped by canons?" That first "a" shouldn't be italicized.

"but none of them was this suicidal" The "was" here should be "had been".

"habits, that would be the Goddess of Hope due to the fact that she was everywhere and everywhen. Well, she used to." The "that" should be an "it", there should be a comma after "Hope", and "used to" should be followed by "be". Also, though this might be personal preference, it might look better if "due to the fact" was replaced with "since". It's more concise.

"barely wide enough as the car" "Enough" should be followed by a comma.

"conceded, “but for" Follow "conceded" with a period, and capitalize "but".

“Those things are Porsche Cayenne Turbos, they’ve got sport suspensions and twice the horsepower we have!” Another comma splice here. Replace that comma with either a semicolon, a period, or most appropriately in this case, an exclamation mark.

"Nikki cast a worried glance behind." It looks as though there's a word missing here, probably either "her" or "them".

"I’m going to take care of them,” Nikki said while getting up from her seat," The second comma should definitely be replaced with a period, and since there are two separate thoughts being punctuated, the first comma could be replaced as well, but that one could be considered correct either way for different reasons. I'd prefer switching it out, though.

"At the joint between the two there were" Add a comma after "two".

"summoned four Barret Shoot projectiles" According to the Lyrical Nanoha wiki, the attack is called Shoot Barrett in English.

"went way off too due to Sergio" Add a comma after "too". Personally, I'd replace "too" with "as well", since "too" seems to me more of a conversational word than a descriptive or active word, but that's mostly just my stylistic choice.

"knocking it out of the chase too" My stylistic preferences from earlier would suggest that you delete the "too" here, making "chase" the last word in the sentence.

"mirror, “how did you do that?" Replace the comma after "mirror" with a period, and capitalize "how".

"over the guardrail as the car chase had a nasty effect on her stomach." To get the simple issue out of the way, there should be a comma after "guardrail". For the second, you might need to rephrase that second part. It's not bad, it's just that, due to an odd mix of definitions and helping verbs, using "had" there would make the grammatically correct phrase in that instance "car chase had had a nasty effect on her stomach", and putting two "had"s next to each other isn't very aesthetically pleasing, at least not to me.

"We’ll try,” Sergio said as he got up and walked towards Nikki and Madoka, “how do you feel?" There should be a period after "Madoka", the "how" should be capitalized, and "How do you feel?" should be followed with an indicator like "he asked the girls." so it's clear that he isn't still talking to Corolla.

Now that those are dealt with, I quite liked this. You don't need to know any of the continua involved to enjoy mysterious and seemingly impossible abductions, magical girls shooting energy blasts from the top of a moving vehicle, and the shipping preferences of omniscient deities. The car chase action scene could have stood to be more dynamic, since at times it didn't feel quite as exciting as a car chase by rights should, but I loved the way you established everything. Not only the setup for the story elements themselves, but how you gave just enough information to show what was going on and why without it seeming like exposition. The only time it seemed a little exposition-y was when Sergio and Nikki were talking about speed limits, but when I looked at that scene again after having read the rest of the chapter, I realized that it was a way of explaining the sort of conditions that would be necessary for a road to contain a high-speed chase, so that passes as well. That said, if this is going to involve enough Madoka Magica material to be considered a "crossover", I might need to get to watching more of the series. I'm going to need to find that Youtube channel that hosted the full season again.

You've done quite the job with Blank Sprite. Even having no knowledge of the Cobra 11 fandom, I did not get lost. Nice work.

A few nitpicks:

Excuse me, I have the last document you requested,” a voice behind them said.
Sergio turned around and recognized the woman as Suzanne König, the chief’s secretary. “The one with the list of their shipments? That was fast, thank you very much.”
Sergio took a quick glance at the document while the secretary walked away. “Well, isn’t that odd. There’s only one shipment on this list, and it’s still at Cologne’s docks. It’s going to be loaded on the ship today.”

In that passage, adding a paragraph break after "secretary" and deleting the break before "Sergio" might make it clearer that Agent Turbo said the "The one with the list" line:
Excuse me, I have the last document you requested,” a voice behind them said.
Sergio turned around and recognized the woman as Suzanne König, the chief’s secretary. [paragraph break]
“The one with the list of their shipments? That was fast, thank you very much.” Sergio took a quick glance at the document while the secretary walked away. “Well, isn’t that odd? There’s only one shipment on this list, and it’s still at Cologne’s docks. It’s going to be loaded on the ship today.”

Also, a few SPaG errors:
The specialized projectile made of wax and powdered iron, despide disintegrating on impact... That should be "despite."

[Then I’m surprised you aren’t going any faster,] Corolla said, [Isn’t that car a BMW?] Should be a period, not a comma, after "said."
This line has a similar problem: [Question: How do we find our container?] Corolla sent out from the RC, [Should we look for a pink and sparkly one?] That should be a period after "RC."

In fact, this type of period-comma substitution happens quite a lot in this story. Please allow me to explain the difference between those lines and this one, where the comma is merited: “A different art style doesn’t change who you are, though,” Sergio said, “or who I am, for that matters.”

In the first two lines, there are two separate sentences separated by the "[character] said" tag. In the third, it's still one continuous sentence; the tag simply went into a space in the sentence. (Without the tag, it would have read, "A different art style doesn't change who you are though, or who I am, for that matter.")

One more thing: you might want to consider hyphenating "less than eager" in the last sentence of the mission.

That said, however, good work overall. I'll be awaiting Chapter 3.