"Yeeeeeeeehhhhhhhhaaaaaaaa!" Asuka exhaulted as her Unit 02 drove 
her weapon through the Angel, neatly slicing itself into half.

You should probably say "drove its weapon" as opposed to "her weapon;" I 
doubt that Unit 02 is using one of Asuka's weapons, (and if it is, then I shall
be very frightened now).
"itself" should be "it"
abd it should probably be either "into two halves" or "in half," the latter
sounding better than the former.

"Yeah! That's all you need- a clean cut!" Asuka boasted as two 
halves of the Angel separated from each other and NERV cheered.

I'm not sure if it really matters, but "as the two halves" sounds better
than "as two halves."  To me, at least.

However, the cheers was cut abruptly as the sliced up Angel 

"cheers were"

shuddered, twisted, and morphed into two separate yet identical Angels.

Once again, not 100% sure it's necessary, but you should probably set
off "yet identical" with commas.

The Children looked around in surprise, "Who's there?"

Keeping the words exactly as you have them here, that should be a
period there instead of a comma.  There are, of course, other ways
to arrange this sentence, (with other words, of corse), and allow you
to keep that comma, if your heart's really set on having it there.  :P

"Oh, sorry. How rude of me." A young boy materialized out of thin 
air in front of Unit 01 and Shinji blinked in surprise. The boy 

You need a comma after "Unit 01" to set off the second independant
clause.

"You're telling me that there's second Angel out there?!"

"there's a second"

Maya nodded grimly. "MAGI has confirmed the AT Field signature, 

I've never seen the MAGI having a singular verb before, but I can see
how it could apply.

He-he just appeared out of nowhere! And it's a BOY!"

I'm going to assume that you wanted the second sentence there to
focus more attention on Shinji'as shock at an Angel being human,
(or something to that effect), in which case, instead of having Shinji
stuttering the word "he," you should probably have him stutter "it." 
<thinks>  Then again, trying to think of it from Shinji's perspective,
that may actually fit.  

"IMPOSSIBLE!" Asuka screamed as she willed her unit to attack.

I can see how "unit" would fit there, but "EVA" or "Evangelion" would
probably work a little better.

Shinji broke in, "What do you want? And how can you talk with us? 

Once again, that comma should be a period.

Kaworu smiled at Shinji, "Oh it's not that hard. It's just that 

Same here.

not all Angels has proper vocal chords to speak, but anyway, I've come 

"Angels have"
Also: end the sentence with "speak" and start a new one with "but."

Gendo stood up, and spoke abruptly, "Put me directly to that 

No comma needed after "up," and the one after "abruptly" should
either be a period, or could possibly be a colon.
Also: "Put me directly to that Angel" --> I can see what you mean
here, but the wording is awkward.  Maybe "Put me through to that
Angel," or "Patch me directly through to that Angel," or something
similar.

Angel, IMMEDIATELY!" Moments later, he was in direct contact with 
Kaworu, thanks to Evangelions' external speakers.

"thanks to the Evangelions'" sounds a little bit smother.

"If you are listening to me, this is Ikari Gendo speaking. You are 
trespassing on private property and committing willingful acts of 
destruction. You are thereby ordered to surrender or face 
consequences..."

I'm trying to figure out if "thereby" is most appropriate in this instance.
The Big Book O' Words defines it as "by or through that," while it defines
"hereby" (the word I was about to suggest as a replacement) as "by or
through this."  Now I'm trying to decide if "therefor" would be a better fit
than either of those two...  *shrug*  Your choice.
Also: "face consequences" does work, but "face the consequences"
flows more smoothly.

Kaworu laughed, "I don't think so. You know exactly why we are 
here, don't you? You've captured Adam, and we want him back. We tried to 

period after laughed
Also: the question "You know....", is he really asking a question to Gendo,
or is it rhetorical?  If the latter, (sort of more like an accusation as
opposed
to a question), then a period would work better there.

check the previous records and you'll see that I'm telling truth. Like I 

"telling the truth"

said, you attacked us without provocation. We had to defend us 
ourselves."

"defend ourselves."

Everybody remained silent as Kaworu continued to speak in his reasonable 
tone, "We tried to enter the grounds peacefully, but you attacked us 

Once again, either a period or a colon after "tone."

every time, and killed each of our brothers. We Angels have come to 
conclusion that you wouldn't be willing to turn over Adam to us..."

No comma needed after "time."
Also: "come to the conclusion"

Klaxons blared throughout NERV as MAGI detected additional AT 
Fields. Afterwards, it was plain chaos.

Normally, I'd suggest "as the MAGI," but as you seem to be treating
them as a single entity, what you have already written works.
Also: "it was pure chaos" seems to fit better.

Unit 01 and 02 were forced to retreat as three plumes of water 

"Units"

erupted behind Israfel. Kaworu introduced each of the Angels as they 
appeared, "Meet Zeruel, Matarel, and... Bardiel."

It's actually "Matarael."  Oh, and I'd really like to see how that thing holds
the bat when it's its turn at the plate.  Come to think of it, how's Ireul
going
to get on the field?  ^_^

Shinji blinked at Bardiel, "Waitaminute... that's an Evangelion, 
isn't?"

Period after "Bardiel," and "Evangelion, isn't it?"

Kaworu nodded, "Correct. Bardiel snuck into one of your NERV bases 

Period after "nodded."

in North America and infected it. Bardiel now lives inside it."
"It's Unit 03, sir!" Hyuga shouted.
"That's impossible! How could an Evangelion have been possessed by 
an Angel?!" Ritsuko protested.
Meanwhile, Asuka and Shinji was feeling rather afraid right now, 

"Asuka and Shinji were feeling"

terror when Bardiel hurled a cylindrical object at their feet. After 
initial screaming, Children realized that it was a...

Should probably be "the Children."

"Well, like I said earlier, since our peaceful methods had failed, 
and you apparently weren't willing to turn over Adam to us, we decided 
to make a proposition to you."

"apparent;y aren't willing" --> while, yes, it was obviousin the past that
Gendo wanted to keep Adam, the Evangelions fighting Israfel also
showed that he isn't willing to give up Adam yet, and it seems more
appropriate that Kaworu be talking about the present situation, as
opposed to the ones long gone, (relatively speaking, of course).
Also: "to make a proposition to you" just doesn't sound right for some
reason.  Getting rid of "to you" makes it sound better, but I'm not
entirely sure that it's the best fix.

Shinji gazed at the Angels in wonder; Zeruel appeared to be snapping 
around an enormous baseball in air, and Bardiel was swinging around the 
baseball bat with its elongated arms. And the Angel which had split 
earlier, now had baseball mitts in their claws.

"gazed at the Angels," or "stared at the Angels"?  To me, the latter sounds
better.
How about "tossing aorund an enormous baseball" instead of "snapping?"
While it still doesn't sound perfect, it sounds better than snapping.
"baseball in the air,"
No comma nedded after "earlier."

Everybody blanched as Kaworu added, "And there's still more of us 
on way..."

"on the way..."

The Angels closed in to the Evangelions as Kaworu repeated his 

"closed in on the Evangelions"

proposition; "We challenge you to a baseball game, and the prize will be 

A colon would work better than the semi-colon.

Silence ensued until Hyuga finally broke the silence, "How many 
rounds?"

Having "silence" in that one sentence makes it sound awkward.  Try "It"
instead of the second "silence."
-----
No, it wasn't *only* C&C...

Darniil Entroth
ccsu0450@earthlink.net

http://www.geocities.com/TimesSquare/Alley/1723/
"Words can be like X-rays, if you use them properly--they'll go through anything." 'Helmholtz Watson', _Brave_New_World_