A beautifully written story! The Second Doctor and Jamie form one of the greatest partnerships in the show's history-I only wish Jamie could remember it...

I thoroughly enjoyed reading this; 10 out of 10 stars!

This was beautiful. Thank you.

This story is very complex and beautifully written, but the errors in dialogue and the lack of commas in certain places make it hard to read.

["Protecting", thought Jamie] should be
"Protecting," thought Jamie

[door, " that's what I'm doing, protecting". ] should be
door, "that's what I'm doing, protecting."

[" Thank you" he called] should be
"Thank you," he called

Basically, you don't need all those extra spaces between the quotations marks and the first letter. Commas or periods always go inside the quotations. Also, you always need some form of punctuation at the end of the speech, you can never have "bla" he said, it must be "bla," he said or "bla!" he said or "bla?" he said.

Dialogue starts a new line, so
[The Doctor had locked him in! " You ungrateful, stubborn fool! What are you up to?" Jamie shouted. Through the windows he could see a figure turn and head away. Jamie didn't know how a shadow could look so craftily pleased with itself, but trust the Doctor to manage it.] should be

The Doctor had locked him in!

"You ungrateful, stubborn fool! What are you up to?" Jamie shouted. Through the windows he could see a figure turn and head away. Jamie didn't know how a shadow could look so craftily pleased with itself, but trust the Doctor to manage it.

Also, when the character says something and then does a non-speechlike action, it's a new sentence, so you make a period at the end of the speech instead of a comma.
(and remember its is possessive, but it's means it is. I think you meant the possessive here.)
[" As much as it can be. This is all I can do, check it's time-pulse" the Doctor gestured to the metronome.] should be
"As much as it can be. This is all I can do, check its time-pulse." The Doctor gestured to the metronome.

Don't use double punctuations
[The Doctor let out a yelp "It's quiet!".] should be
The Doctor let out a yelp. "It's quiet!"

Correcting the dialogue will make the whole story much easier to read.

Finally, sometimes you're missing commas. Commas denote pauses and certain phrases need them

[It's astounding what the right whisper will do when applied with the correct amount of emotional leverage isn't it Doctor? No you never ask directly, but then that's not the way you operate.] should be
It's astounding what the right whisper will do when applied with the correct amount of emotional leverage*, *isn't it Doctor? No*,* you never ask directly, but then that's not the way you operate.

I would recommend having someone give you a read through for all of the tiny stuff.
. . .

And now onto what I loved about it!

-"Its journey began from suns that burnt long before gunslingers slung or *R*omans conquered or Mona Lisa thought it would be a very lovely day to sit for a painting"
-Jamie insisting on calling his sneaking protecting.
-"Jamie didn't know how a shadow could look so craftily pleased with itself, but trust the Doctor to manage it."
-"doctoresque contraptions"
-The Doctor referencing the jabborwock
- this lovely speech: "And it's my Tardis." *T*he Doctor whirled *around.* "Mine. My Tardis that's flown and sung through purple suns. That's danced on the shock wave of the big bang. It's tumbled and twisted through the cataracts of Volturnus and blazed across time, and it has to fight. I need it to fight. I need it to live-"
-And not to mention: "It wants me to let it die. To turn off the equipment and let it go. But I can't. Don't you understand*?* You may have given in, but I won't. Life *is* life and I will fight and burn and rage for it. I'll *(I'll means I will)* do everything in my power to protect it and yes, I will scheme and lie and cheat for it too."
-Really dazzling imagery throughout.

Wonderful story!

That was beautiful, thank you for sharing it.

So nice to see a second Doctor story and with Jamie too! I could picture this playing out as I read it, and yes I can believe this of Stonehenge having visited it many times... or should that be her?