Okay, this damnable game goes two ways depending on whether you choose to play as X or Zero:
A military based group called "Repliforce" (led by the gentle giant "General" and his second hand, "Colonel") is wrongfully blamed for the collapse of the Sky Lagoon onto a crowded city. Ticked off, the group declares its independence from humans and the Hunters. The Hunters don't like this idea of seperation (thus beginning their tarnished reputation), and decide to take action.
X returns to Hunter base, and finds a cute little reploid named Double waiting for him. Double declares himself as a rookie Hunter who was assigned to help X with his missions. X accepts this and goes about his business, destroying awry members of the military group.
As luck and Megaman Logic would have it, Double's name serves a purpose. Taunted by some Hunters one day, Double transforms into an ass-kicking reploid and extracts revenge that high school nerds can only dream about. In the meantime, X learns about the "Final Weapon," a massive gun in outer space that is built with the intent of aiming at the earth. As he rushes to stop General, he meets up with Double, who announces he was a spy for Sigma this whole time, mwa ha ha. X is noticably upset at being tricked by a friend he trusted. Double says tough cookies, and attacks. X rips him up, and storms off to find General.
X eventually finds him (God, he's two storeys, he's not about to hide under the table), and insists he's doing the right thing for reploid-kind. X says no, and since X is always right, the two fight. The Hunter wins...but at a price. The Final Weapon activates itself with the help of...who else...Sigma.
X takes on Sigma, and the dialogue between the two is slightly uninteresting. They fight. X wins, of course, but Sigma declares that nothing can stop the Final Weapon from destroying earth, mwa ha ha.
General appears on the scene and decides to redeem himself for doing something as awful as engaging in free thought. He uses what's left of his battered body to destroy the Final Weapon. Hoorah!
X flies home and is contacted by Zero. X asks Zero, "What if I become a Maverick?" Zero uses the word "baka" somewhere (yes!) and tells him to just come home. X, however, makes Zero promise that he'll destroy him if he becomes Maverick.
And, given that X wasn't SUPPOSED to be able to go Maverick since he was the only "properly" constructed Reploid (Cain modified Light's notes to make the others), the overall story of the X series takes one more baby step into the realm of "WTF?"
Zero's story is quite a bit more detailed. Zero is haunted by nightmares of a crazy man with crazy hair in a crazy labcoat. These dreams usually involve blood and things that scream. But he always wakes up before he can get a clear picture.
Again, there's the nasty business of the Sky Lagoon crashing into the city, and people die and stuff. However, as Zero searches through the carnage, he finds Iris, the sister of his friend Colonel. He rescues her from a massive Dragon Mech. After the battle, Colonel appears and says hello to Zero. Zero asks if Repliforce is occupying the area where Sky Lagoon crashed. Colonel says no, you big blond wookie, I was just looking for my sister.
Nevertheless, Zero asks Colonel to disarm and follow him back to MHHQ. Colonel refuses, saying soldiers never disarm. Zero warns that Colonel and the Repliforce will be judged as Mavericks. Colonel leaves in a huff.
Repliforce, declared Maverick, announces its independence. And, as in X's story, the Hunters don't like it and decide that something has to be done about such an awful thing.
Zero returns to MHHQ and finds Iris there. She's obviously smitten, and she doesn't want Zero and her brother (Colonel) to fight. Zero says what has to be done, has to be done. And he goes after the 8 Repliforce warriors mentioned in X's story.
After defeating four of the warriors, a message comes into MHHQ. Colonel wants a fight with Zero. Iris begs Zero not to do it. Zero tells Iris to feck off by running off and doing it anyway.
Zero gives Colonel one more chance to redeem himself and mispronounces 'coup.' Colonel refuses, and the two fight a sabre battle which Iris breaks up in the middle. Iris pleads with her brother, saying that Zero saved her life. Colonel agrees to break it up, but warns of no mercy next time. Iris asks Zero to drop the fight with Colonel. Zero says no, and goes on to defeat the rest of the warriors.
With the Mavericks taken care of, Zero learns about the Final Weapon--and decides he has to take down Colonel. He hunts down the officer, who seems stoked to fight. Zero reminds Colonel that Iris would be sad if he died. Colonel tells him to shut up and fight. They do. Zero prevails, but Colonel doesn't think so. He died with honour, which is all he really wanted, and tells Zero, "tell my sister I died happily."
Zero goes back to MHHQ to deliver the bad news, but Iris isn't anywhere to be found...and the Repliforce is getting ready to move to the Final Weapon, and have to be stopped. Zero scrambles.
Upon landing on the Final Weapon, Zero finds Iris. He starts to apologize for Colonel's death, but Iris won't listen, and says "it's all over." She transforms herself into a gargoyle mech, and attacks Zero. Zero has no choice but to subdue her.
Iris lays on the ground, fatally injured. Then begins a death scene that's touching until Zero starts to talk. Bad voice acting aside, Iris tells Zero that she wanted to live with him in a world where only reploids exist. Zero tries to tell her such a thing will never exist. Iris says maybe, but it was a nice dream. Then she dies and Zero screams and stuff.
Zero finds General and informs the giant that innocent blood is on his hands. General says maybe so, but independence has a high price. Zero attacks him. The fight's a real bitch with Zero's crumby range, but it's easy to win with some practice.
As in X's story, the Final Weapon activiates itself with General's defeat, and Zero must fight Sigma.
So. Zero meets up with the scarred one. And he learns some interesting truths about his past (see X1's summary for the scene). Zero's not too surprised that he was a Maverick in the past, and true to his former nature, he still loves to fight. He challenges Sigma.
Sigma goes down, but Final Weapon is still about to blow. Again, General uses what's left of him to stop it. Zero escapes in the nick of time. On the way back he has some lonely flashbacks of Iris and decides that maybe all reploids are Mavericks after all. Whatever that means.
A great game, all around. It was the first X game on the PSX, so the sprite changes were refreshing. It's very solid, and a fan favourite all around. The ability to play as Zero is very hoorah.
My only real complaints lie in the sound. First, the voice acting. Though not nearly as bad as Megaman 8's, it's pretty pitiful at times. See, the voices are just fine for the most part (better than the Japanese ones in many places--except for X of course), but the acting was nonexistant. And it's embarassing to play a game where the voice actors are obviously struggling to read something off a paper. Give yourself a treat one day and watch the Japanese anime videos. I give their Zero an A+ for his psychotic screams and laughs alone.
I also should complain about the anime in this game, I guess. I don't find it's nearly as smooth or well done as Megaman 8's. Kind of grainy. Sticks in your esophogus.