The prolouge, with my critique. My comments are in
blue
A young she-cat
It flows better if you say "Female" shivered as she trekked back to her den. She walked slowly in, careful not to disturb her day-old kittens.
A tom cat watched her from the corner as she sniffed a mouse he had brought, she gulped it down eagerly, not looking up until she had finished.
This is a run-on sentence, and should be broken up into two. Example: "A tom cat watched her from the as she sniffed a mouse he had brought. She gulped it down, not looking up until she had finished.
“What will you do with them?” asked the tom cat.
“Who? The kittens?
Of course she knows. Maybe it would be better if the tom cat had said "what will you do with the kittens" I’ll find someone to take care of them.”
“They are very little you know, you shouldn’t do this
Do what? Get rid of them?.”
“I must.” Was the she-cat’s blank
Blank means empty, or clear...I'm not sure what you mean by this word here. reply, she had to, but didn’t want to.
Another run on problem. too many commas.
The tom shook his head, “You saw them, none can escape their grasp, the kittens will die without you… Please, Rita….”
I'm confused. Saw who? Who is they? They'll die without her? I know you are trying to make it mysterious, but I'm more confused than anything.
“Jako I know you think it’s foolhardy that I might be able to get them out, but I can, I know I can. My one regret is that I’ll never see them become what I hope they’ll be.”
“And what is that?”
“Warriors. Warriors who can defeat Cogg and his army.”
“That is impossible! Rita, use your head, these little ones,” his tail swept over the kittens, “Are only babies, they won’t be warriors, they may not even live!” hissed Jako.
“Jako, I must get them away. Please help me.”
Jako sighed and reluctantly agreed.
Why is he reluctant? He wants them to live, right?
That night the two cats readied themselves. Rita took the first kitten, a golden haired beauty, whose fur shown in the sun.
Took him how? With her paws or in her mouth?
“I shall name you, Toto, you are my firstborn. Be a leader.” She whispered to the little cat, who wasn’t even a week old, but seemed to hear his mother’s voice, as he let out a soft mew in acceptation.
Jako stayed with the others until Rita came back. Rita then took the next kitten.
This one was dark haired and beautiful, one who blends with the shadows.
“I name you Caspian, be a protector and a kind boy.” She whispered, and again the kit gave a small mew of exception.
Then the next kitten, a pale blond-golden haired girl who wriggled with anticipation.
“I name you Dorthy
Dorthy and Toto? No offense, bit it's a bit silly to name them after the Wizard of Oz. It makes it much harder to take this scen seriously, be a strong girl, be frightened by near nothing, have defiance and stubbornness like your mother.” This time the kit mewled loudly, Rita stopped a moment, then continued quickly.
Then the last kit, this one was the very tiniest kitten of all of them. She had dark hair and Rita carried her lightly and sang,
“Little one, little one, be greatest of all,
Let none bother you because you are small,
Be kind and sweet,
Though small and petite,
A tiny kitten,
The toughest,
Most defiant,
May the Lord King be with you,
Ever, always.
Mozart the Meerkitten,
My baby.”
Why does only Mozart get a song? And why is she a Meerkitten? (is that explained later) I doubt very much that cats would know about human composers....
Anyway, I'm sorry if this seems harsh. I am not trying to be mean. I'm just being honest and trying to help you improve your writing. You have an interesting idea and a cute story, and I'm certian that someday you'll be a very good writer. However, even a good writer can improve. Keep writing. 
