The True Nature and Intentions of Sephiroth [Spoilers]

[The Crystal]

Before you can discuss that, you have to clarify who you mean.

I've played FF7 many times over, and what I've gathered is that when the story begins with AVALANCHE destroying the No. 1 reactor, at that point in the story, the man Sephiroth is dead. He died when he fell into a Mako Reactor, after putting a large sword into Cloud. My understanding is that Sephiroth was a powerful man, capable of doing things that most humans could never do. But he was still a mortal man with limitations almost identical to the average human.

If that's the case, how does one explain the Sephiroth you see in the game at various times, like on the boat from Junon or in the Forgotten City, descending from above with the afforementioned large sword?

That being is actually Jenova, I think. And that's the Sephiroth that you chase after. That's the one who can fly and stuff. Humans can't hover like that. The real Sephiroth was no exception.

So..... The real human Sephiroth who died a while ago wasn't a bad guy initially. He learned where he came from, and it drove him all kindsa crazy. His crazy angry-at-the-world rampages ended with his death, in the Mako Reactor.

But the Jenova Sephiroth is totally different. That one is always babbling on about the planet and the Promised Land and such. It's not angry at the world like the real Sephy was. It is simply doing what it feels is right. That Sephiroth has nothing but good intentions in that he is setting things the way they should be.

So to call him a good "villain" seems stupid because someone with intentions like that isn't very "villainous". In fact, upon completing the game, you're left to think that perhaps Sephiroth/Jenova was right. Perhaps the world needed these things to happen like Meteor and such to make things right. According the Sephiroth, the humans were responsible for the disappearence of the Cetra, who rightfully should've been living on the planet. If that's the case, that would make Sephiroth/Jenova the good guys and Cloud and his gang would be a side plot of sorts. I think Cloud's not concerned with the justification of the humans or any of that. I think he's concerned with stopping a world threatening catastrophe at the moment, and then he'll sit down and figure out the philosophical and moral rights and wrongs after the eminent threat is gone.

It seems that you didn't understand some things. In Nibelheim, Sephiroth was exactly like you said. A guy that wanted to avenge the Cetras because the humans killed them. He wanted to do this, because he thought that he and Jenova were Cetras too. BUT what you have to understand(and remember) is that after Sephiroth jumped(retconned in LO) in the Lifestream(in Nibelheim) he learned many things in the Lifestream, and gained the knowledge of it. And with the knowledge of the Lifestream, he learned about Jenova's true nature(a "calamity from the skies"(alien) capable of controlling its cells(Reunion), that killed the Cetra), like you can see her:

"Cloud: Sephiroth!

Sephiroth: Being here brings back memories. Are you going to participate in the Reunion?

Cloud: I don't even know what a Reunion is!

Sephiroth: Jenova will be at the Reunion. Jenova will join the Reunion becoming a calamity from the skies.

Cloud: Jenova, a calamity from the skies? You mean she wasn't an Ancient!?

Sephiroth: ...I see. I don't think you have the right to participate. I will go North past Mt. Nibel. If you wish to find out... then follow...

Cloud: ...Reunion? Calamity from the skies?"

Sephiroth already know that he and Jenova aren't Cetras, and he don't want to avenge them(the Cetras) anymore. What he want to do, is absorb all the Lifestream of the planet and become a god. But if he absorb the lifeforce of the planet, the planet and all living beings in it, will die.
And do you think that Sephiroth don't know this? Of course that he know, but he don't care. He just want to become a god, and will use anyone to do it, even his "mother" Jenova(the Ultimania Omega Guide said that Sephiroth was controlling Jenova's body with the power of his will).
Sephiroth don't care about the humans, the Cetra, and even Jenova, he only care for himself. He is evil and don't have any "good intentions". He want to become a god, and will kill anyone in his way to achieve this. Simple as that.

I think I recall reading that Sephiroth is biologically the child of Hojo and Lucretia. I do remember something about Hojo messing with him while he was still in the womb. But how does Vincent fit into that scenario? And what about Professor Gast? I know he was this brilliant researcher, but what did he uncover? Or what was he working on? I know it relates to the Cetra, because I seem to remember him being married to Ifalna, whom I seem to remember being Aeris's real mother.

Vincent was a Turk that fell in love with Lucrecia, but she choosed Hojo. Then, she became pregnant of Sephiroth, and both of them decided to inject Jenova cells inside of Sephiroth's body, as a part of an experiment.
In the begining, Gast(that was working in the project), Hojo, and Lucrecia, thought that Jenova was a Cetra, and wanted to make Sephiroth be like a Cetra, to help Shinra to find the Promised Land. But after some time, they discovered the true nature of Jenova, and discovered that her cells enhance human's capabilitys, because Sephiroth was becoming more and more powerful. Because of this, Shinra begun to inject Jenova cells in SOLDIERs.
Gast was the guy who found Jenova, and was part of the Jenova Project, with Hojo.

And while I'm getting all FF7 philosophical, I have a few questions that I haven't gotten figured out yet. Did Nibelheim really burn down? If so, why was in totally good shape when you arrive there in the game? And why does no one there recall the event taking place? And if it didn't burn down, then why does Cloud think it did? And why does Tifa think it did? When Cloud tells the story at the Kalm Inn, Tifa doesn't object to it and seems to sit silently as Cloud talks about Sephiroth burning down a city.

Sephiroth burned the town, but after this, Shinra tryed to hide the incident of everyone else, and because of this, they build all the city again, exactly like it was before being burned. Then they put actors in it, to pretend that they allways lived in Nibelheim, and pretend that nothing happened.

So that brings me to my next question. Was Cloud really an experiment? I know he probably got the Mako Treatment like other guys in SOLDIER, even though I think he was never really in SOLDIER. But was he really part of Jenova like Sephiroth was? Did Hojo or whoever actually inject him with Jenova to try and create a superhuman kinda guy? He did go totally crazy when he was with Zack heading to Midgar, when Zack died. I'd think that might be a side effect of the Jenova infusion thing. But that would mean that he didn't really grow up in Nibelheim.

Or maybe he grew up in Nibelheim, left to join SOLDIER, and then they did their weird stuff to him and it made him all crazy.

After the Nibelheim incident, both Cloud and Zack were injected with Jenova cells. Hojo did this, because he wanted to test his theory about the Reunion. Hojo knew that the Reunion would happen, and because of this, he injected Jenova cells in the citizens of Nibelheim that survived Sephiroth's attack, to study them and the Reunion process(these people were the black cape guys/girls). Zack and Cloud were part of this experiment.

And why does Cloud think that he was Zack in a lot of his stories? You find out that he was a Shinra guy, but not in SOLDIER. So how did Cloud get to thinking that he was Zack in all those stories?

When Sephiroth, Zack/Cloud and two Shinra guys go to Nibelheim (during the Kalm Inn story), Tifa talks with Cloud during that visit, and even guides them through Mt. Nibel. You learn later that Cloud was there for that visit, but Tifa never knew because he had his helmet and mask on the whole time.

Because of the experiments in Nibelheim. Cloud and Zack were injected with Jenova cells and Mako, and this made Zacks memories go to Cloud's mind. And because of Cloud's weak mind, and his desire to become a SOLDIER, he convinced himself that that memories were his owns, and he was a SOLDIER.
And Tifa knew that Cloud was there, because of the retconn in Last Order. But the explanation of why she didn't told Cloud during the game, is not revealed.

And the Weapons? What's their deal? Are they the planet's self defense mechanism? Their come out when someone is messing with the Mako levels and just level the world, Mana Beast style?

If i remember well, they were created to fight against Jenova, but she was sealed, before their activation, and because of this, they weren't used. But is like you said, they are the planet's self mechanism of defense. Their objective is to destroy everything that is harming the planet.

And is true that you played the game many times? Because some of these questions are very well explained in the game, and i don't understand how you could have missed them.