If I were suggesting how to improve this mission, my number one recommendation would be: work aggressively in Third Person Limited.
You've come close to this. Most of the story, we seem to be sitting solidly on Silver's shoulder - but occasionally we wander off. You're halfway between Limited and Omniscient, and it drags the story down.
So make it strictly Limited. That means: anything Silver doesn't know, we don't know. If you have thoughts written in - 'This was it. Ceka shows her true colors.' - they can only be Silver's. If someone is away from Silver - such as Ceka immediately before that line - we don't find out what they were up to unless they tell Silver.
And the flip side of that is, we delve significantly deeper into Silver's mind. You've added a subplot about Silver hating (and fearing) new things, but it makes almost no impact. In aggressive Third Person Limited, we can see all the times Silver glares at Ceka, or thinks she's untrustworthy. And through Silver's eyes, we can see her gradually come to trust Ceka. At the moment, she suddenly trusts her out of nowhere; we should have seen that building through the entire mission.
To show you what I mean, I'll throw up an example of 'strict Third Person Limited' for the Ceka-bothers-the-Doctor scene. Please don't use this; it's just intended to show what I'm talking about. Based on your text, of course.
Anna broke down in sobs, pulling Silver’s attention away from the cringeworthy ‘interactions’ of the Doctor with the unoriginal characters. She patted Anna on the back, trying to comfort her, but not getting very far: how could she, when she was in need of comfort herself?
Anna was still sniffling when the class ended. Flier and Angel went… somewhere, the fic wasn’t at all clear.
“It will be all right,” Ceka said to Anna, sounding distracted – as if she were planning something. Silver looked up, and her suspicions were confirmed: the Time Lady was already sprinting away towards the school door.
“Running off again,” Silver said in a low voice. “Do you know if we’ve got a way to contact the DIA on short notice? I’ve a feeling we might need them.”
Anna lifted her head from her knees and gave Silver a surprisingly sceptical look. “You know she’s just trying to finish the mission, right?”
“After all those protests about not wanting to write charge lists?” Silver countered. “She’s up so something. We should never have brought a Time Lord into a mission with others of her species; she’s probably plotting to take over HQ with them.”
“There’s humans in the story, too,” Anna pointed out. “Are
we planning world domination?”
“That’s different,” Silver objected. “She-“
There was a rush of footsteps, and Ceka lunged around the corner of the building. She dove beneath the window, and Silver jolted to her feet, hand on the hilt of her dagger.
“Where did you go?” she spat, eyes blazing. This was it – time for Ceka to show her true colours.
The Time Lady stopped dead, taking a deep breath, and then that eerie calm descended on her features again. “Oh, I was just checking up on the Doctor,” she said, her voice much too casual. “It seems that he is possessed when the Twins are around.”
“The Twins of Doom,” Anna muttered, climbing to her feet and wiping her eyes. She shot a look at Silver –
I told you so.Silver was less than convinced. She was hardly going to
admit to helping the Twins, was she? “Don’t run off again,” she growled, glaring at Ceka – who returned the look, with interest.
Anna’s voice suddenly broke the silence. “Character bios incoming.”
Silver had no time to react. The bios pummelled at her ears, an aural assault that forced her to her knees, and it was no consolation that Ceka was suffering just as much.
As you can see, I've completely removed Ceka's excursion - we're sitting on Silver's shoulder here. I've also done my best to eliminate things happening to
them - instead, our Limited viewpoint sees them happening to Silver,
and to the others. Since Anna's behind her, she actually doesn't notice that she's gone down as well at the end - only Ceka, who she's facing.
My rule has been to try and have a Silver-perspective in every single paragraph. Sometimes it's because she's the one speaking, of course. But other times - the description of Ceka's demeanour as 'eerie calm' and 'much too casual' - her impressions colour the narrative. Sometimes it's even more subtle than that - 'Anna's voice broke the silence', rather than 'Anna', because the silence is in Silver's ears, and she's not paying attention to Anna right then. So what she notices is the voice.
This can be hard. It's much easier to just slip into reporting the bare essentials - lines of dialogue traded back and forth. But that pushes you ever closer to MST style. I'm not saying Silver should colour
every line - but she should be doing so more often than not.
(I've gone with Silver because, like I said, you're most of the way there anyway. But this story would be equally interesting from Ceka's shoulder - trying to befriend someone who's irrationally suspicious of you - or Anna's - trying to make Silver see reason about Ceka, who's actually quite nice)
hS