A military and mystery work? We'll see how this goes.
I now can see that you actually tried to format your story now that I have it in a quote box, with the indentions and all, but the forum takes that all away. Instead, adopt the forum formatting and double space between paragraphs. It's easier to read that way and it's just basic formatting since indentions don't really show up.
"Watch your language Lt. Kamos." Scott Mitchell looked at the large wooden vessel that seemed to be just drifting. "Damn! It's so old its got freaking oars!" he muttered. As the sound of whirring helicopter blades became louder as the cruiser got ever closer.
Mitchell is a hypocrite. Stupid old hypocrite. Anyway, the bolded part is a sentence fragment. Just combine the sentence with the previous sentence, adding a comma after "muttered". Or, just take out "As". It would be like this:
The sound of whirring helicopter blades became louder as the cruiser got ever closer.
It sounds more clean and crisp now.
The two AH-73s hovered above, an invisible x-ray beam shooting down from both of them, providing necessary information to the commanders in the bridge, who relayed it to Commander Mitchell.
Seeing as I have no idea what an AH-73 is, I'm lost other than that they are some kind of helicopter or something. I'm still lost on the x-ray beam as well. It just kind of needs a small little explanation for clarity, because knowing what an AH-73 is is not exactly common knowledge. The next bit is that there is just an excessive use of commas, it's just listing stuff. It's not exactly violating anything grammatical, it just doesn't flow.
"Okay boys, and girl," he started, acknowledging Olivia, "this hear is a tireme, tiream," he zoomed in on the information panel,
For the bolded part, I have no idea what you're trying to get at here. My best guess is that he has no idea what a "trireme" is, so he can't read it correctly. It's vague when there's not much description, mainly referring to the character's actions and his body language which would tell readers he's confused.
"a trireme. This boat is about 2490 years old! Damn! I have no clue how it stayed intact so long, but its here. It should be around 120 feet lo-!" he was cut off as an update appeared on his screen.
The correct form is "it's", since that is the conjunction of "it is". Its would represent possession, which would be irrelevant here.
"Damn! This thing is 500 feet long! The tallest mast alone is 182 feet high; add that to whatever is below the mast, that's about 272 feet! Damn! Lt. Riska will take over from here." The young Russian man stepped up and aimed a portable projector at the side of the bridge. It showed full schematics of the trireme.
Damn! Damn! Damn! See how annoying that is? Leave a bit out. I mean, it's just a ship. It's like the guy has never seen a boat in his entire life.
"This is a 100 oar ship, 50 on each side, four floors including the deck. It is only 100 feet shorter than this boat comrades, it is very large. There is a single, seen, large spike jutting out the back and there are no signs of life being picked up, not even rats.
The first bold shows that "it is very large" is in a comma splice, as the sentence the comma combines them with has two independent clauses. Replace the comma with a semi-colon. For the next part, I'm confused with the "seen" in the sentence. It looks like the word is just dropped in there. You could just omit it.
David asked Shawn as they chainers extended the wide steel walkways.
Probably a typo, but it should just be "the".
"Watch your footing!" she said without turning around. David played innocent.
He played innocent, but I have no idea how he did so. I can assume that he just looked away and whistled. I can assume he turned away and looked at the lapping of the waves as they hit the old boat. I can only assume. Be sure to describe it more.
"Don't touch that for two reasons," he grabbed the younger mans shoulder, "it's probably diseased, and it's a skeleton. That would be disgusting."
Forgot the apostrophe there, so it should be "man's".
"Their all from different time periods. This one is obviously from around the time of the renaissance. It is wearing knights' armor and it has a long sword and kite shield. That skeleton over there however," Riska pointed...
You want to use the form of "they're" because that is the conjunction of "they are".
"That didn't sound natural…" Olivia said tentatively. Her com piece suddenly was suddenly filled with the sound of helicopter blades and Marina's voice.
Suddenly was suddenly. What? Omit a suddenly.
"I thought you guys didn't pick up anything on the x-ray or radar!" another marine shouted into his own com.
I'm iffy on these. It's just repetitive. You could just leave it as "his com". I mean, he wouldn't shout into someone else's, would he?
A loud crunch was then heard and three pale white tentacle type things shot out of various points of the boat.
The bolded part, "type things" tells me that you can't adequately describe your monster. That tells me a lot. I know you can describe it. You created it. Don't use that bolded text. It kind of discourages readers.
She looked up and saw that the blades had stopped just at the right spot that she could eject. She looked at the emergency button, and then hit it.
Yeah, for that very reason, helicopters don't have an eject function. The blades would slice you up. The most sensible would be for the pilot to go into a hard landing, but seeing that she's being grabbed by a monster and is in the middle of the ocean, it doesn't look like a good option. I guess if she unstrapped herself and just jumped out of the side, at least it made sense.
So before the above quote, you had a rather long part about how the marines were firing on the monster. Not much description other than, "the marines shot at it. The tentacles waved like they were in a rave and smashed the mast. The marines shot more. The helicopters fired misseles, somehow missing the marines on board and keeping the wooden boat intact. Modern technology was at its greatest now. Marina screamed in her com as the tentacle smashed against her window. The marines shot some more."
Okay you didn't really say that, I added in some of my flavor, which was more for my entertainment than yours. I can have fun too right? But it's really boring to read that. Add in description. I can't stress it enough. You have solid action, but there's almost no images. All I can do is assume what everything looks like. Use your five senses and put that onto the computer screen.
That's all I can say, or feel like saying, for now. So be sure to keep in a few facts in mind and remember to proof-read. You have a few grammar mistakes and typos, which are actually one-time occurrences since I saw that you had the correct usages somewhere else in the chapter.
Good luck and keep writing!