Part 1: Mission 1 - Prologue (PS2 Version)
Here are our two protagonists: Hugo Medio and Aqua Centrum. Unlike MX’s predecessor, Alpha 2, you don’t get to choose – both are coming with us. Oddly enough, they take the time to point out the characters’ age, even though you can’t change it: Hugo is 20 while Aqua is 23.
It should also be noted that this game skipped custom birthdays for special spirit commands (I’ll get to these soon, if you’re not familiar). Still, Hugo and Aqua’s default lists complement each other very well.
What you DO get to choose, however, is the unit they’ll pilot. Do you want Garmraid, the close-range Super Robot of fangs in its rocket punches and saw blades in its knees (you do), or Cerberus, the long-range Real Robot with a big gun (boo!)?
The story is 95% the same regardless of the unit you choose, though the first two missions change. I’ll be playing through both these first ones and then progressing with Garmraid through the rest of the game – no, you don’t get to object! I love this ridiculous mech!
It’s possible to alter the mech’s name, too, but I’ll stick with the default ones.
And here’s our cool team.
Finally, you may choose one series as your favorite (three in the PSP version) and all units of those series will enjoy a 50% boost to exp, money and PP earned while also getting two extra upgrade bars.
I had a vote when Z was ending and the thread went for G Gundam.
With that done, let’s get to it.
Do note that if you're on the PSP version of this game, you'll want to check THIS prologue. There are quite a lot of differences. 
Seventy years after the inception of the Space Calendar, a series of events irreparably shook the fate of mankind.
Creatures from a parallel world, the “MU”, suddenly appeared in the skies above Tokyo and engaged in battle with forces of the Earth Federation. This conflict, expected to become a world-encompassing war, reached an abrupt end when the MU erected an unknown sphere around the area, centered on Tokyo's bay, shutting themselves inside.
Right after, a large asteroid struck the South Pole – a catastrophe later dubbed the "Second Impact" – which inflicted immense destruction on mankind and threw the Earth Sphere into chaos.
Mankind weathered the "One Year War" and the "Lizard War", and when peace seemed at hand, the Earth Sphere was engulfed simultaneously in the "Gryps Conflict" and "Devil Gundam Incident". Compounding matters further was an invasion by aliens known as the "Baam", intent on colonizing the Earth.
Meanwhile, the "Mycenae Empire", "Devil Empire" and "Dinosaur Empire" also began their assault. As the Earth Sphere's fate hung in the balance, the efforts of the Federation, the AEUG, Super Robots, the Nadesico B, and the New Shuffle Alliance proved sufficient to repulse all the attackers. A peace accord was struck with the Baam, while the Neo Zeon Army, which sought to act in the aftermath of the Gryps Conflict, was soon defeated.
However, the embers of war were not extinguished...
With the declaration of war by the lunar Giganos Empire, assaults by mysterious foes known as "Angels", numerous UFO appearances and elusive shadows surrounding the Hisago Plan, mankind was about to step closer to its doom...
Prof. Mitall Zapato is talking to a certain mysterious woman, noting that everything seems to be going according to plan. The Medius is ready for launch, but what of its pilot?
The woman says he’s already on standby at the rendezvous point, and that she and AI1 should be able to handle things until they reach him. Furthermore, she asks for confirmation that the Garmraid/Cerberus’s pilots are, indeed, Hugo Medio and Aqua Centrum. And, yes, they are.
She seems a bid uncertain about this choice and Mitall admits that results haven’t been the best so far. That said, he chalks it up not to lack of skill on their part but of the TE Engine’s low output. Or, perhaps, is the mystery woman feeling a wee bit guilty?
No, she says she merely wants “her child” – AI1 – to have suitable opponents. Mitall does sigh that she kind of IS the thing’s foster mother. Regardless, the woman asks why the TE Engine was installed in that machine – if he’d let AI1 handle it, it’d be getting far better results than those two.
Mitall says it’s a small handicap, as the balance of forces between is already askew. To say nothing of the fact that AI1 wouldn’t really be able to make sense of the DFC System. The woman calls that system absurd, depending on sensorial input for control.
Whether she likes it or not, though, Mitall says Aqua's data is vital to AI1's long term success. She disagrees, saying that all AI1 and the Lazmunanium need to display their full might is a perfected TE Engine. Still, Mitall and those two are needed to make that happen, so she’s little choice.
Either way, it’s time for them to get to work. Mitall then confirms her two targets: the Nadesico B and the Nahel Argama. According to the Committee's script, those two ships are bound to be the focal point of a major deterrent force and keeping them tagged will let them gather a whole lot of useful data. The woman concurs and moves to close in to them.
Mitall starts to tell her that he expects good results from her, but reconsiders and says that it's enough if she's able to prove his theory. He isn’t planning on sticking with “them” until the end.
Elsewhere, we find Aqua accosting Hugo. She wants to know why he didn’t do as she said in the test they just performed – he received the data she sent with the drones' counterattack motions, no?
Hugo points out that all drones were shot down in the end and with eight seconds shaved off the time too. What’s the problem? The problem is that he went and acted all on his own and she wants to know why.
And she won’t take no for an answer – she won’t accept any more tests going the way of this one. Their mission is to produce the results Mitall is seeking, Aqua reminds him. Hugo’s a bit miffed when she brings up the professor.
: But, regardless, I want you to stop ignoring my instructions.
: I’m keeping them in mind, you know.
: Oh, keeping them in mind, are you? But, of course, who am I to say anything to Mr. “Ex-Special Forces”. My instructions are clearly not worth much to someone like you.: I didn’t mean it like that. It’s just…: Just… what?
: Were that an actual fight, we would have ended up a crater in the ground. That’s what I thought.
: …!: …You should just focus on managing the TE Engine’s output. I’ll handle the Garmraid/Cerberus in battle.: Well, excuse me for not having any actual combat experience! But I’ll have you know that, eventually, I’ll be piloting the Medius and—
: Hrm…?!
: What is it?
: N-nothing… Sorry but can you grab me a glass of water?: Huh? What am I, your waitress?!: …Please.: F-fine… Just water, then?: Yeah…: (Gch…! And things were going so well with this…): Here – your water.: Sorry for asking…: Hm? What’s that?: It’s just… cold medicine.: Cold, huh? I guess you’re more delicate than I thought.: …Is that a problem?: Not really.: (There… It’s stopped…): Well, just make sure you get better quick. I really don’t need you getting me sick, too.: Says the one walking around in a swimsuit. How can you not catch a cold?
: This is a DFC Suit! Not a swimsuit! A DFC Suit!: I know that.: Bah…! I’m not wearing this because I like it, alright?: Still, you seem rather OK with it.
: Well, sure, I can just jump into the bath with it and…: B-but that’s not the point!*BOOM!*
: What?! An explosion?!: It came from the hangar!: You think it’s the Garmraid/Cerberus?: How?! Both of us are here!: Then it’s the Medius Locus…?!: That can’t be either! They haven’t even chosen its pilot yet!: Well, first things first – we need to find the professor right now!
*ALARM!*
: Urgh! The hangar’s hatch was destroyed?!: What’s going on, Professor?!: It’s the Medius…! Someone’s stolen it!: !: Oh, no…! Who could do this?!: We’ve no choice – you two must pursue it. If that unit falls into enemy hands, it’ll be a disaster…!: R-right…! If the Lazmunanium is misused, we could potentially see a repeat of the Devil Gundam Incident from a year ago…!: (The Devil Gundam…!): Understood, professor! We’ll get the Medius back in our hands!
: Please do. The Garmraid/Cerberus will be ready to launch soon and, if need be, you’ve permission to destroy the Medius.: Y-yes, sir!: I’m counting on you.
: (Yes, very much so… Hmhmhmhm.)This prologue here is the same regardless of which robot your choose.