*le bow* Thank you!
Also, I have to admit, I wasn't planning on writing much more in this universe, but I'm sort of tempted to do so now to cover incidents involving different SEs.
And that's the only non-spoiler-riffic thing I can say right now! :D So here's a spoiler tag~!
Also, yep, the creature is Mewtwo. Basically speaking, this fic takes place in a world where all of the legendaries and other strange and supernatural phenomena/cryptids/what-have-you occur. The organization in question (yes, it has a name, I swear) is a hybrid of the SCP and the Men In Black. Their duty is to contain basically everything that humanity shouldn't know (still) exists, including and especially the embodiments of nature/legendary Pokémon themselves. So, they're not actually Team Rocket; they're just really pissed off that Team Rocket created more problems for them (and tends to do that a lot because Team Rocket is like "lol science").
As for why Leaf (and the entirety of Cinnabar Island) had to be erased from memory, it was so people wouldn't get curious and attempt to find Mewtwo. Because you know there's some jackass out there who'd be like, "There's a Pokémon that ****ed the champion of Kanto up? Let's go catch it!" Because the organization realizes that humanity is a psychotically moronic species. So the story goes that Leaf was removed from public memory, Red was instated the champion (with the story that he went to Mt. Silver to train, not because he went effing crazy), and Cinnabar Island was volcano'd out of existence to thoroughly cover up the idea that there's a Mewtwo out there. Like, Mewtwo is basically a Keter object, and for whatever reason, people like to play with the Keter objects. Like Leaf did before it mind-controlled her and had her beat the ever-loving crap out of Red with a flashlight.
So they're hoping that by covering up this incident like all hell, no one will attempt to find Mewtwo. They're also hoping that if no one attempts to find Mewtwo, Mewtwo won't mind-control them and break out/make them [DATA EXPUNGED] hang themselves with their own intestines.
Fun fact? If you know how to read little bits here and there, the story becomes clearer. For example, the heading for each scene actually tells you most of why this is happening by itself. Take the first one for example:
INCIDENT SE-004-03, FILE 4, EXCERPT 1
And compare it to the last one:
INCIDENT SE-004-01, FILE 1
How do you read these? Well! "INCIDENT" is pretty straightforward: it's noting this as a chronicle, a record of materials that describe what happened in a containment breach or any other event in which the subject displays its power. "SE-004" is the name of the object; the "SE" stands for "Special Entity" (not something I mentioned within the story but would be cool to know maybe), while the number stands for its number in the organization's index. So, Mewtwo is the fourth Special Entity recorded by the organization. (Note that it goes in order of recording. That's why Mew is SE-005 while Mewtwo is SE-004. The organization could not verify Mew's existence before Mewtwo.) "FILE #" and "EXCERPT #" both indicate similar things. In the first case, the audio transcript was the fourth document included in the materials describing the incident involving Leaf, and the first scene of the fic is the first excerpt from that particular document.
What's not straightforward is the number after SE-004. That's the first thing that changes between the headers. For most of the story, the full incident name is "SE-004-03," but for the last scene, the number is "SE-004-01." Why did it change?
Because that's the incident number.
As in, that's the number of times a similar incident involving that object occurred.
As in, the story isn't describing the first or second time Mewtwo went on a murderous rampage.
If you let that sink in for a bit, that might help you understand why the story had to happen.