Nintendo 64

Yes, it was pretty much a straight up grade on anything that needed improvement and they kept anything that worked. Story got just as confusing towards the end as the first one, I don't really understand MML's overall plot.

I was so young I don't think I really cared about the plot too much.

All i remember was

I might get load up an emulator and give it another go.

Do not play Legends on N64. It has significant glitches that the PS1 version doesn't. Might as well play the PS1 version anyway, since MML2 is only on PS1, which means that if you start on N64, you'll have to relearn all your muscle memory to play the sequel anyway.

Very.

Have you played the rest of the series? The general idea of what's going on during MML2 is understandable if you pay attention during MML2. How things got that way is never specifically explained in the Legends series, but there are hints in other entries throughout the rest of the series. I can explain things, if you have questions.

explain

Explain what? Everything? That'll take a pretty long time. I'll start with some important points. All spoilers in this post are actual spoilers.
MML1 has very little in the way of story, and really just sets the tone:
Humanity is stuck collecting "Quantum Refractors" which are an energy source and a type of money from underground ruins that exist for unknown reasons. These are probably the result of the Ciel System from the Zero series.
There's a rumor of a really fucking huge refractor somewhere, colloquially referred to as the Mother Lode.
Space stations controlled by robots periodically genocide people within specific geographic regions, for some reason.
Data has administrative control over those space stations, and gives you control of the one the boss owned after you kill him, but doesn't explain how to use it.
For some reason, ancient peoples were aware that Mega Man would exist.
In the time frame of Legends, Mega/Rock Man isn't a name of a specific person, but a title.
MML2 actually has significant backstory:
The Mother Lode is not a treasure, but a kind of doomsday device.
The biggest robot space station and administrative center, Elysium, is implied to be the creation of X. This is mentioned in the bad end of X5. It is run by an administration of advanced robots with strict roles. Known roles are Mother, Purifier, Bureaucratic, an Servator units. All units that exist are subservient to humanity, and the supreme leader is a human known as "The Master" who looks suspiciously like Zero. In Japan, Purifier Units are referred to as Irregular Hunters, which is the same term as Maverick Hunter in America.

The exact purpose of Elysium is unclear, but is implied by the existence of the Earth's population, and the way that population is treated. They're referred to as "Carbons" by the inhabitants of Elysium, and "Betas" by the owner of Elysium, implying that they're not actually human. In Japan, they're called "Decoys." They were created by the people on Elysium, and are not actually human, but cyborgs that are part biological, part machine. Their easy swapping of bodyparts isn't a special technology that they've developed, but a part of their basic form. The way they're treated, genocided and studied in cycles by Elysium's administration, implies that they're part of an experiment. It's unclear what they're testing, but the most likely option is that they're testing to see if the Earth is habitable again after whatever catastrophe led to the global flooding. The ruins over the world are just remnants of the human civilization that fled, and the Reaverbots therein are just workers and security systems. The refractors are just the power source for them.

The human population of Earth was evacuated to Elysium at some point, and their genetic codes were stored within a library. Their absence on Elysium is highly suspicious, since humans are supposedly immortal while there, which also raises the question of why they needed the genetic library in the first place. Once certain conditions are met, a system called the Carbon Reinitialization Program is meant to be activated, which would kill all Carbons on Earth, and respawn all humans who lived on Elysium back on Earth via their genetic codes. However, the genetic Library is incomplete, as the genetic sample of Elysium's leader, The Master, is in the hands of Mega Man/Data. (cont.)

(Cont.)
At an unspecified point in the past, a Maverick Hunter named Trigger, was best friends with The Master, who outlived all of the other humans, somehow. Because Elysium is a proper utopia, with nothing to do or struggle against, The Master became so disillusioned with life that he asked Trigger to accompany him to Earth to observe the Carbons, which was also essentially suicide for him, since it also meant leaving Elysium's life support. Observing the Carbons, who lived lives filled with suffering, that were more "human" than those on Elysium, he came to the conclusion that they'd made a mistake somewhere along the line. Realizing he was about to die, he asked Trigger to destroy the entire system, in hopes of correcting the mistake, implying that the Carbons should be left to continue their lives without their interference.

Trigger returned to destroy Elysium, but was opposed by Sera, the Mother unit of Elysium. Because of the ambiguous nature of the situation, Yuna, the Mother unit of Earth, chose to take a neutral role in the fight. Trigger and Sera fought to a standstill, which Yuna used the opportunity to seal both of them in stasis and repair/reset them. It's unclear why she decided that neither side should win at that time.

An uncertain amount of time later, Baryl Volnutt finds a child in stasis in the ruins at Nino Island, along with a robotic monkey. Mega Man Volnutt is the reincarnation of Mega Man Trigger. Baryl isn't really his grandpa and Roll isn't really his sister. He seems to retain his combat experience in his new form, but nothing else. Data is essentially a sentient hard drive that has all of his old memories, as well as the authorities that Trigger had over Elysium's systems, and exists to assist and protect Mega Man.

Likewise, Sera was sealed in the same way, but on Forbidden Island, which is where you go towards the beginning of MML2.
I've written a lot. You getting all this?

Yea… Holy shit I had no idea it actually tied back to the X series. I thought it was "Megaman" only through character design.

Sounds like the second game went pretty far off the deep end though.

Sounds to me like you haven't looked that deep into Mega Man. It's not just Legends, the entire series is jam-fucking-packed with lore, but in a way that never requires you to know it, so it never gets in the way of gameplay.

Besides the cutscene in X4, was there any other indications that zero killed all the original characters? It never really shows what happened to them and… well.. if that were the case it'd be pretty badass.

The only evidence for that theory is that everyone is missing. There's no specific evidence for it, and the man who would know, Inafune, specifically denied it. Additionally, it doesn't make sense from a timeline perspective, if you take into account that's Zero's ultimate purpose wasn't to kill Mega Man, but to grant Dr. Wily immortality by spreading the virus. Which is naturally at odds with letting Zero loose to kill Mega Man before either project is complete.

i ordered an s-video cable to maximise sexiness.

I guess I forgot to say that I play the games on my phone with a snap-on gamepad.

Super Smash Brothers

You just named the entire Rare replay collection. You should play NBA jam 99

Star Fox 64

Has a shitload of replay value. One of my favourite games of all time.

this. If you haven't played a pure upper track while saving all your bombs for andross, you haven't beaten it.

Mario kart 64 was my fave Nintendo 64 game.

Most of the good exclusives have been mentioned, but also consider:

Diddy Kong Racing
South Park
Star Wars: Rogue Squadron
Star Wars: Shadows of the Empire
The New Tetris
Mischief Makers

Mine survived a house fire. Still plays well to this day.

Pretty much the only game I keep my real N64 around for instead of trying to emulate it. Never feels right in emulation.