The fanfic chapter in question if from "Of Gods and Mortals" by Matthew Regent. The passage I am wondering about is as follows:
"HEY!" yelled someone. I jerked back as a series of crashes landed on the TARDIS doors. I moment later I realised that that it had been Haruhi knocking. Can't that girl even knock normally!? "IS THERE ANYBODY IN THERE!?" If there was somebody in here do you really think they would want to open the door to that!? A few seconds later the door handle began rattling as Haruhi tried to swing open the door.
Ha Ha! Fast facts here people, the Time Lords were the first race to exist in all of space and time. They possesed immeasurable power and could have easily turned all of creation into their own playground if they wanted to, not that they did. due to their own non-intervention rules. Anyways they had been around long enough to locate beings like Haruhi every once in a while, and they worked out ways of dealing with them.
First things first their very existence and technology were already pretty much immune to them because Haruhi and her kind are reality-warpers (for lack of a better term) the Time Lords existed outside of reality. To put our situation in simple terms it was this, the TARDIS enters time by writing its existence into that time, transferring it's existence from the Time-vortex into said time, essentially what Haruhi does whenever she activates her powers (although she uses her powers to write her ideas into existence rather than pull objects from the Time Vortex), however the TARDIS is a reality unto itself, it's actually bigger than earth inside.
It's difficult to explain how it works in human terms (look, you get it eventually, I haven't turned into some kind of Alien since I left) but essentially the TARDIS has to constantly maintain this reality within itself separately from the outside reality, the junction between the two being the exterior and doors.
Okay, if you actually understood all that you're doing better than most people. Now onto how this actually affects my current situation, since anyone who enters the TARDIS and is accepted by the telepathic (it not actually telepathy but once again, difficult to explain) computing system in the TARDIS and given the ability to understand all languages then you are effectively a part of the TARDIS's reality as well, and thus are maintained to a certain extent from the effects or time-shifts and reality changes because the TARDIS protects your original existence like it does with it's own.
Basically the TARDIS posses a limited version of Haruhi's reality warping powers. Hers change reality while the TARDIS maintains it's own. If she tries to change anything consciously or otherwise relating to the TARDIS, myself or The Doctor the TARDIS will cancel it out. It even works outside due the fact the TARDIS links itself to you to translate everything so technically you are a part of it via that link and thus you're safe, even when you are not technically inside the TARDIS.
So, presuming you managed to get all that, it means: Haruhi is trying to open the TARDIS doors. The TARDIS doors are locked and her powers that would normally somehow open the door for her are blocked by the TARDIS. Thus there is no way she can get in.
Dammit now I'm sounding like Koizumi!
"OPEN THIS DOOR! I KNOW YOU'RE IN THERE!" Keep your voice down dammit, my ears are getting sore...
"I beg your pardon Suzmiya-san but perhaps there really is no one in there, in which case we should get going-" Koizumi was cut off at that point. Just for the record, do you know how incredibly creepy it is to heard somebody you knew a long time ago and their voice hasn't changed one bit? At the very least it makes you feel damn old...
"What! No, there's something fishy about this box and I want to know what it is!" Oh just go with him Haruhi, you don't want to come in here! Well actually you probably do but I don't want you to come in here!
"Suzmiya-san!" Squeaked a quiet voice. "T-the neighbours are giving us funny looks..."
".. FINE!" Haruhi snapped. "But I'm coming back later and this box had better still be here when I get back!" A moment later I heard the familiar sounds of her stamping feet as she walked off in a huff.