I'll briefly go over the first few pages, it should help to give you some ideas.
It doesn't mention the actual story, it reads like a potted history of the Ninja.
The logline is your pitch and should tell the producer four things:
Genre, budget, audience and appeal.
Genre=can it be sold? Check.
Budget=Can it be made? Can't tell.
Audience=Who is it aimed at/who will watch it ie demographics Check. Males 16-35.
Appeal=What in the film appeals to that core demographic? You've not put in the appeal. Is it a martial arts film, a romance? etc
You need to put more in about the scale of the film. It could be a film about a single ninja attacking a castle which would mean that despite the period setting, it could be a relatively low budget. Conversely it could be on the scale of the Last Samurai
. OK, it's an epic story, so get that point across in your logline.
People have a general idea of what a ninja is, so tell us the exciting things. Who is the main star, what is his mission, who he has to fight.
INT. SMALL ROOM. ODA?S CASTLE ? NIGHT
The audience only knows what we are shown on the screen. Remember SHOW NOT TELL. All we would know is that three samurais are sat in a small room. We wouldn't even know they were in a castle.
You would either have to start with an EXT. of the castle to establish the scene or have a SUPER on the screen ie a Subtitle reading Oda's Castle 1603 or whatever.
If ODA is important, I would suggest that you introduce him quite quickly.
Initial Impressions. Good atmosphere. The period and the characters lend themselves to interesting stories. There is a mystique about Ninja's and Eastern Philosophy which adds to their reputation as fighters.
You should name your Samurai's. It is confusing to read numbers. They are also important characters so should be given indivual names. Only walk on parts/extras should be numbered IMO.
I'd start the film with them talking about the girl. Mention the thunder storm after the opeing conversation when they've started to spook each other out. (Now that I've read more, it seems strange that you mention the girl but then not have her come into it much at the beginning)
There are some contradictions in your description of the ninja's. They are supposed to be invisible but this guy saw one. If you want to maintain their aura then I would remove the fact that he saw one. Everyone else died and he didn't even see the assasin.
OK. I've read the first 30 pages.
1. Dialogue. Too on the nose. Also it can be very long in places and too much of the story is being told through talking. Find ways to get the information across visually.
2. Characters. I believe that we are introduced to too many charcaters too quickly. We don't have time to get to know any of them. Masaro is your main guy so concentrate on him earlier.
The samurais at the start of the film are being used to introduce us to the history of the ninja's. The script feels like it is trying to teach us who everyone is rather than showing us what they do and what they are trying to achieve.
3. Structure. Too convoluted at present. It's hard to get a sense of what's going on. It's like you are withholding information to ensure everything is a surprise but it makes it difficult to follow the motivations of our key players.
These are some very general thoughts but I hope they may be of some use.
I'll try and add to it at a later date.