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Part 17: This is not a Drill
Man, Lan's been hanging on that cliff for a while now, huh? I suppose I should continue this sometime this century.
As it turns out, Mamoru is not the administrator of the Undernet. However, he is the son of the Undernet's administrator, and thereby inherited the responsibilities that came with that.
Presumably Kimie is aware of this as well, but, well... this is a "shonen" kind of series. It wouldn't at all be surprising if Mamoru manages this secret server all by himself since parents aren't allowed to do much of anything. Let alone mothers.
Isn't that right, Haruka?!
More to the point, who's ready for some deep lore about the Undernet?
As Mamoru explains, the Forbidden Program had the power to freeze Alpha. If its power was misused, however, it could freeze over the entire internet. As a result, they needed a rather large space to isolate the program, hence the Undernet's creation. And its distance from the main Internet meant that it eventually became a safe haven for bad guys. Which was probably fine with SciLab in the end, given the notorious reputation of the place would likely keep people away.
While Mamoru doesn't go into his role as administrator too deeply, presumably he oversees the ongoings of the Undernet to make sure they don't get too close to the Forbidden Program. This will later be even more strongly implied once we meet Serenade.
But enough about that. It's time we finally learn about our enemy.
Well, we knew that much already.
That, however, is a new tidbi-
Wait, but what about the exposi-
Battle Network 3! 
So, while MegaMan was acquiring the Forbidden Program, important developments were ongoing in SciLab Area 1.
It's a fairly short video, but the gist of it is that DrillMan stole Alpha.
You know, this thing that we saw forever ago!
Yeah, the final boss has been right in front of us the whole game. The early Battle Network games were really good about leaving big things in plain sight, though this isn't quite as subtle as the Kotobuki stuff from the last game. Still, points for effort.
At this point, I feel like the gin rummy family knows more about the plot than Lan does.
This guy's still pretty clueless, though. Good job leaking government information, you dip.
As it turns out, the government officials are totally flabbergasted that Wily managed to put together the most obvious plan that you could make and never thought to, I dunno, call in the Officials to defend Alpha. (On that note, where the heck did Chaud go?!)
But I think we've long established that the people in this universe don't brain good.
Honestly, why are you adults so useless? You're a government facility guarding a global threat. This is downright embarrassing.
Anyway, as it turns out, DrillMan Gurren Lagann'd himself to the other side of the internet when he stole Alpha, and it's up to us to go after him.
This wormhole stays here for the rest of the game, incidentally.
Which is convenient, seeing as it's a shortcut to the Undernet!
This guy also moves now, allowing you to reach the UnderSquare easier. How convenient!
At any rate, MegaMan soon catches up with the perpetrator. As usual, the preceding cutscene will be shown in the video below!
Boss Fight: DrillMan
Oh boy, it's BubbleMan's cousin. I sure hope he doesn't have a gimmick as obnoxious as his predecessor. Certainly not one that, say, requires a very specific folder build to fight him with? To deal with the fact that he's only onscreen for very short periods of time? And also always moving? And also blocking all attacks from the front with that huge, impenetrable drill on his head?
Because it'd be REALLY annoying if he had those multiple gimmicks all at once, with no warning whatsoever!
- Drill Drive: DrillMan drills into the battlefield through three holes, one on each row, at different timings. One of these drills is DrillMan, giving MegaMan the opportunity to damage him. The drills can be destroyed with breaking attacks.
- Triple Hole: Three holes appear at the back of DrillMan's area, and they constantly fire drills down random rows. One of these holes is linked to DrillMan - shooting it will damage him. Once again, the drills can be destroyed with breaking attacks.
- Panel Crusher: Three panels on MegaMan's area will flash. DrillMan will then drill through these panels, destroying them, and three rocks will fall on MegaMan's area.
After that... experience, Lan and MegaMan decide to talk about how bad things would be if Wily got Alpha.
Good thing Wily didn't get Alpha, though, right? Let's just stand here and talk about how bad it'd be if Wily got Alpha. While not, y'know... actually grabbing Alpha. Surely nothing will go wrong.
Oh... Hm.
So that whole Giga Freeze thing kinda went nowhere, huh?
Yes, it was entirely pointless! And never comes up again! Well, aside from a side-game that never got brought overseas. And a fan-made Hard Mode battle against Bass.
But yeah, that's a nice little capstone to this whole arc, huh? We went through a whole Undernet Ranking to get a MacGuffin that Bass stuffs into his pocket and forgets about, while also learning barely anything new about the main enemy of the game. Everything's pointless, Wily wins anyway.
The end! No moral!