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Alright, was hoping I'd find some place to put these ideas down and get them organized. Warning to anyone reading this, I've beaten the second game and this has spoilers...probably a lot, so you were warned, don't read if you dont want them.
First, the setup for the third: Obviously based on the end of ME2, the Reapers are on their way. Shepard's still got time cuz they're coming in via their own power, but they're awake and moving nonetheless. Also judging by the closing scene, there's a lot of Reapers. Sovereign was just one and he decimates the Citadel and multiple fleets. His pinky cracked off and almost killed Shepard in the first game for crying out loud. So, now with a whole flip-ton of them coming, obviously fighting is not gonna save the day. So, how will Shepard beat the Reapers?
I believe Bioware has already given us bread crumbs towards the answer here. I believe the answer lies with EDI. Yes, the AI now controlling the Normandy. Why would I think this? In ME2, after her safety protocols are removed, EDI mentions she has access to "Anti-Reaper Algorithms." This is odd, thinks Shepard, as the Reapers are millions of years more advanced than us. How could a human made AI construct hope to fight them? He asks this, and EDI explains that she is based in part on technology recovered from the wreckage of Sovereign. She's made with Reaper parts. Shepard doesn't probe into this any further (for which I insulted his intelligence, since it seemed pretty darn important to me), but the hint has been dropped. My guess, is that they will beat the Reapers with EDI, either via a computer virus, a reprogramming, or some other cyber trick. It makes logical sense too. There's not enough munitions in the galaxy to beat these guys physically, they've been killing organics for millions of years without mercy, so we can't negotiate, Shepard has to land the killing stroke, because its his (and your) game. So how can one man defeat multiple giant evil spaceships without a gun or talking his way out of it? EDI's nifty computer virus, or whatever it is they come up with of course!
Now, the game wouldn't be an epic conclusion without a battle, and let's face it, even if the computer virus had flashing lights and a sense of humor it would still be pretty dull to watch on screen. Imagine, a fleet of dark and mighty Reapers, closing in, then Shepard pushes the button...and they all die. Hooray galaxy! Boo fans! So, in keeping with the whole Star Wars trilogy analogy people are throwing around (you know, ME2 is the "Empire Strikes Back" of Mass Effect thing), I predict an epic Return of the Jedi style space battle in ME3. Who will fight in this battle? Well, there's where you come in.
In ME2, players are tasked with assembling a team of diverse species for a suicide mission. What if, in ME3, you are tasked with assembling an alliance amongst species to hold off the Reapers while you personally deliver the virus? Again, I'm not basing this on nothing. In ME1, you had the option of making an ally of the Rachni. They're building ships in ME2, according to news reports. When will this matter? In your epic space battle in ME3! Who else will show up? Well, the council and Alliance owe you, but if you're still not on speaking terms, then perhaps Cerberus? Oh, and don't forget the Krogans and Geth. Why would they fight? Oh, maybe because you reprogrammed the Geth to fight Reapers in ME2! As for the Krogans, they're uniting behind your pal Wrex, and you have Dr. Mordin Solus working on that Genophage cure for them of course! Granted, all these things depend on your choices, so you might show up with no one to fight for you. If you've made friends though...Imagine, the Geth, the Rachni, and the Krogans, three species the galaxy united to try and put down, fighting at your side against the Reapers. All you have to do in ME3 is seal the deal with these good folks.
As for returning characters, well, who on your team survived? Is Mordin alive to work on that cure? Did you get Tali killed, and now have the Migrant Fleet peeved with you? I think any surviving characters from ME2 will have a role, even if it is a small one, in ME3. As for ME1 returns, I already guessed Wrex would come back leading his people to battle. Liara's an information broker now. A powerful ally in your line of work. As for Ashley/Kaiden...I'm not quite sure. Lol, I have a hope and a guess, but its a long shot. I think Ashley/Kaiden is either a spectre now, or the human equivalent in special forces. Why is this? Well, their mission on Horizon was very hush-hush, and they seemed to be the only one there. They're military types, so why weren't they with soldiers, either with a unit or commanding one? My guess is they're covert spectres now. The Council is being sneaky about a second human spectre due to the trouble they had with you, but they couldn't be so stupid as to think you were imagining Sovereign's attack. Even if the Council is that stupid, Anderson isn't. Ashley/Kaiden are special forces for either the Council or the Alliance, and they've been working on the Reaper problem too, but on a different angle from Shepard. I think this would be SO epic, to have your former second in command return as an equal willing to work with you (provided you didn't cheat on them), but that's Bioware's call. All of this is. I'm just a peddler with a crystal ball, shouting out his own ideas.
Feel free to use this, any Bioware employee who sees it. Just remember me when I come knocking on your door for a job lol ;) Alright, let me know your ideas for ME3, anyone who reads this, I'd love to hear them =)