After defeating Donte in FA 2003 I would have Ed join the Templars

Love each the story so far. So can't wait for the next chapter. An very well written and funny 2.

...I can't even think of a good comeback. Fine, I'll sit here a little longer, maybe collect dust while I'm at it...

Bah! I'll try and live a little longer, hollyleaf. Although I'm certain you're joyful to have been given some reprieve from an awful reviewer such as myself.

Hooky leaf, it's me, aqua alchemist alpha. I can't send pm messages, and my old account is unnecessarily. I wanted to let you now, and this is the only way that I know how to. Help me. Please. Add me as your friend. All of my work is gone. It's me though.

You gave me permission, so I'm going through this entire thing. *Laughs maniacally*
'Amestris didn't even have buildings close to this high of magnitude.' The sentence is really awkward at the end. Perhaps, '...buildings close to a height of this magnitude.'
'The free fall and pulled a cord...' You switched tenses. Fall should be fell.
"I'm not used to this advance of technology..." '...technology this advanced,' might work better.
'Technology sucks at times.' Tenses were switched again. Sucked, not sucks.
'Wait till you see the pieces of Eden...' For some reason, when certain words (like until, because, and others) are contracted, the contractions are written like this: 'till, 'cause, etc.
'...Ed said recalling past memories like homunculus.' That sentence is very awkward. It's just... Meh. Homunculus should also be capitalized.
"It's should be towards your left side..." 'It should be to your left...'
'Ed and Desmond landed safely and quickly unhook the parachutes off.' Another awkward sentence; '...unhooked the parachutes,' would have been enough.
"Many of which is the apple." I'll admit that I don't know if apple should be capitalized, but the sentence disagrees with itself. 'Many being apples,' would work better, because there are multiple, separate apples of Eden.
"How can you be so quite?" This one's actually a common mistake. You want quiet, not quite.
'Ed and Desmon walked with the crowd as they walked by wagons selling suevinors.' Try, 'The pair walked with the crowd past several wagons selling souvenirs.'
'Desmond ducked behind the wagon and barely glance to see the Guard obviously a Templar standing there.' Another awkward sentence. Guard also should not be capitalized. 'Desmond dove behind the wagon with barely a glance to the guard - who was obviously a Templar - standing nearby.' Yeah, some detail was added, but it also made it clearer.
"...Find the managers office an from there, the safe and apple should be in there..." And is missing a d.
"Kay." This is another one of those contraction words. Okay, shortened, is 'kay.
'Ed and Desmond walked over to the Employee's Only.' Employees, not Employee's, and you forgot the word door.
"Man, that bastard better not had all the fun..." Better not have all the fun, you mean.
'Ed turned a hallway and mentally smacked his forehead In LARGE BOLD lettering...' Turned the corner, and you forgot the period between forehead and In.
'...a voice alerted Ed to turn around..." The voice isn't telling Ed to turn, is it? '...a voice said, alerting Ed. He turned around and...'
"Yes Indeed." Indeed does not get capitalized. It's not special enough.
'Logan shouted pointing a finger at Ed who was standing there cross armed.' Or, with his arms crossed.
'Desmond nodded as they flee through the doors.' Another tense change. Fled, not flee.
'They walked up to William, Rachel,' ...And who else? If there's no one else, then the word 'and' should be between the names, not a comma.
"...The apple is something that I have close to nothing on knowledge of it." That's another weird sentence. '...The apple is something I know next to nothing about.'
"...Well they never exist on my side." Existed, you mean.
'Ed said thinking of city behind Amestris.' Xerxes, the city Ed was thinking of, was beneath Central City.
"Anyways, we have to go found out where to find the uranium bomb...' Consider, 'Anyways, we have to go and find out where the uranium bomb is...'
"I will try and speed up the process so that way we can find out about the location." 'I'll try and speed things up so we can find where it's been hidden.'
'It had only taken a few days to go ahead past six years just after they left Munich.' This is another really weird sentence. Maybe you were aiming for something like this? 'It had only taken a few days to skip another six years, after Ed had left Munich.' Presuming Desmond hadn't been in Munich, of course.
'They had been able to miss much of the parts because most of them were harder to access but they had to watch his death by Envy, his dead half brother.' Let's try, 'They had been able to skip past most of his memories, but they had been forced to witness his murder by the hands of his now-dead half-brother, Envy,'
Okay, I know I already recommended a beta. And I'm pretty sure you said something about getting one. So... I think you'd prefer long reviews that wax poetic on your ability to write and your creativity, not about the spelling/grammatical errors that someone as picky as me had caught while reading.

THATS IT? NOOOOO

Yay. You made more. I love you. This has to be the BEST crossover ever. Just because of this, I'm going to make my own assassins creed crossover. AAAAAAWWWWSOME!

HEY LOVE BOTH CROSSOVERS MAKE MORE MORE MORE MORE

2. Hohenheim left before 1904, when Trisha died (Ed: 5, Al: 4) but it's often presumed Ed was 4 and Al was 3, because when the clip is shown of Hohenheim leaving, Al has a pacifier. Both ages are acceptable.

High school? Eh, not questioning it. It's summer where I am, so...

"Huskisson…" the kid came down the stairs and looked at him who was gapping in awe. "You made two mistakes."
Gapping should be gaping.

I see your point. Makes sense, but it brings up the question of why he had never used it before, and how he did know how to use it when Desmond asked. But since he can, what would Roy be? An enemy and an ally, or just one? Or maybe a special target, since they always seem to make it a point to argue... I thought that I should say that, in the manga and in Brotherhood, Ed was born in 1899. Has nothing to do with this since you're going by the 2003 anime, but I felt like mentioning it.

You're killing me, hollyleaf. A beta, which is pronounced like the Greek letter (you know, like how alphabet comes from the first two letters, alpha, beta,)and is essentially an editor. A beta reads the beta version of a story, the unedited version and edits it, gives their input on certain scenes and such. Once the beta and the author agree on the story or chapter, the author publishes the alpha, or finished, version of the story/chapter. It's really the same as what goes with publishers.
And I don't know too many good FMA or AC betas, I'm sorry. I tried getting help once with something I wrote and it took my about five different authors and about six months before I got an edited version. But that was a completely different fandom and I'm certain you'll have better luck than I did. I just sent my request to all the wrong betas, ha-ha...
There's a beta selection on the toolbar at the top. It lets you search for betas specifically by category and fandom, as well as rating and genre. It would probably be best to search for someone who has experience with both fandoms, so its as accurate as possible.
Good luck on your search.

Hey holly beta readers are like co-authors and help others like when u help me on my story's and I help u on yours

You're welcome. You said you needed help, so I just wrote out whatever came to mind. All right, let's see... There's really no way I can tell you what to do. Going back far enough to do all the episodes will mostly depend on whether you want it and if it's important to the plot. If you want it there, then it wouldn't be so hard to work it in. And would it have anything integral to the plot? If Abstergo has anything to do with the Homunculi or the Gate, or if tehy have to do with the First Civilization, then that information would be important and would save Ed the trouble of explaining it all to them. If they don't, then skipping would be a lot easier since they don't need to know so much of Ed's past. It depends on how you want to spin this.
So, write whatever takes your fancy. I have noticed a few mistakes here and there, so a beta might be helpful, and they're usually willing to let you bounce ideas off them. So, until then, I'll sit back, relax, and let you take this wherever you please.

No no no no no no noes. No.
Alright, taking a look back at chapter 1, you could go back a little farther and introduce how Ed learned about the Assassin's and became one himself? Why would that happen? If you've played or read about AC1, Desmond can't skip ahead to the memory that Vidic wants him to see because Desmond's subconscious isn't prepared for such a jump, and Lucy had to ease him into it, which took just about the entire game. A similar situation can be applied because the Animus: may bot be able to handle the appearance of the Gate; speaking with Truth could lead back to when Ed first performed human transmutation, which was very traumatizing and force him out of the memory like Desmond did in AC 1; or the Truth/Gate could interfere somehow and cause some sort of accident.
Why does all of this go on? Since this is the first anime, this has the Thule Society and giant dragon-Envy. Quite simply, put them with the Templars and you have a nice, bloody shindig. They could fight, they could come to an agreement or alliance of some sort, they could kind-of assimilate and become one organization altogether, you name it. What I do recall from the 2003 anime is that the Thule Society was trying to open the Gate. Why don't the Templars try their hand at it? Does the Gate have any connection to the First Civilization and/or why they fell? Is the Gate a product of the First Civilization, maybe a last-ditch attempt to preserve their technology? If so, was it sent to Amestris? Why can Ed use alchemy in wherever he is? Is the world he was sent to (Nazi Germany) have anything to do with AC; I mean, is Nazi Germany part of the past or is it an entirely different world? If they're one and the same, then why can Ed use alchemy? Does it have to do with where they are? Like, if there's enough of the First Civilization's technology nearby, can it allow for Ed to use his alchemy (and maybe augment it?) If not, can he use his alchemy elsewhere? Are there others who can? Is it possible there are others who can also use alchemy?
Really, I'm just listing off ideas here. Use whatever you want or don't. I don't care, I just want to see this finished. Have fun with whatever you do.