Is Kadaj the only Sephiroth?
During the confrontation scene with Rufus, we see Kadaj show his true colours in being a Sephiroth clone. And he was the one to dip into Jenova cells and become Sephiroth. But if Loz or Yazoo had gotten to them could they turn into Sephiroth too? Initially, they're all clones, right? So they each have an equal chance of being Seph, Kadaj just got to the cells first, right?
Technically, they're not "clones", but rather "Remnants", manifestations of Sephiroth's will. As you can see especially clearly in ACC, though they assume physical forms, they're not entirely corporeal beings. This is how they form their clothing, how Kadaj enters Healen through a closed door, how they insert materia into their bodies, and so on.
Since the Remnants are essentially just "Sephiroth's will", it's really not that different from what Sephiroth does throughout much of FFVII with Jenova's body, controlling it with his will and even having it take his physical appearance.
But, in short, since they're all made of Sephiroth's will, any one of them could have "become Sephiroth" with Jenova's cells, yes. As Kadaj personified Sephiroth's charisma and ability to lead, he was naturally the leader of the group and Sephiroth's primary puppet, as well as the one which had the greatest understanding of his own situation as Sephiroth's puppet.
How do they know Marlene is with Tifa?
After the fight with Tifa, Loz speaks to Kadaj/Yazoo and says "All right, I'll bring the girl." But how do they know Marlene is there, much less who she is. And why do they need her? When she's at the scene at the Forgotten City, she just stands there. She has no Geostigma.
I believe the intention was to use her as a hostage or bargaining chip, not neccesarily anything deeper than that.
Why doesn't Tifa get Geostigma?
After Cloud runs to Tifa while she's fainted and he starts to have a relapse of the stigma, his arm starts doing the melty thing. It's clear that one gets the Stigma from direct contact, and he's leaning right over her. Granted his arm is supporting her, but it leaks from all around his arm. Why doesn't she get it?
Geostigma's not contagious, regardless of how some may think it came across in ACC. In the world of FFVII, it was originally believed to be contagious, and there are probably still some who think it is, but it really isn't.
Geostigma is actually not an infection, but rather an autoimmune disease. The bodies of those afflicted try in vain to fight off and expel the foreign cells, damaging themselves in the process, resulting in the black puss-oozing stigmata that give the disease its name. It poses more of a threat to children, the elderly, and people with frail bodies, though the concentration and amount of Jenova cells in the body are also factors. For example, Ruvie was more-or-less killed instantly when the Lifestream passed through her body.
Kadaj is flaming.. is he gay?
At the Forgotten City, Kadaj starts bursting into flame when he's speaking to the children. Is this his limit break? Is that how he expels the black stuff into the water? Also, what IS the black stuff? The children already have Jenova cells in them from the stigma, so what's the black stuff they're drinking?
People seem to generally assume that it's either a Limit Break, or just a sign that he's activating the ability.
The black stuff is the manifestation of Sephiroth's will, the same stuff that formed the Remnants and their clothing. When the children drink it, it "activates" their Jenova cells. This not only cures their Geostigma (because their bodies stop rebelling against the cells) and increases their physical capabilities, but also allows them to be directly manipulated and triggers the Reunion instinct in the Jenova cells, which Kadaj hopes will help him find Jenova's head.
What Materia was affecting Loz/Yazoo?
When Cloud comes in on the crew, we see a glow of materia as Loz and Yazoo are shooting at him. It seems to be boosting their power/shooting. But what materia does that? o_O
Various support materia, most likely.
Which lake is it?
Are the lake that the kids drank at, and the lake where the phone drops the same connected lake? During different scenes we see large bodies of water that all seem to be connected to eachother. However when Cloud's phone drops into the lake, and we get an underwater view, it's very much a deep deep small circular lake that doesn't get much shallower. That's gotta be where Aerith was laid to rest... But ingame, Aerith is laid to rest in the front lake, which is where the kids were drinking the water. *confusion*
The pool of water Cloud's phone drops into is a different one. The lake the kids go into is the one where Aerith was laid to rest.
THEY ARE TAINTING HER RESTING PLACE!!!
Yes, Kadaj taints her resting place with Sephiroth's will. He also kicks over Zack's sword and tramples the flowers in the Sector 5 church -- all of the places most closely tied to Cloud's guilt, where the symbolic wolf appears.
Coincidence? Unlikely.
How familiar is Marlene with Vincent?
Marlene goes and runs behind Vincent's cloak, when Cloud's being a douche. But how familiar is she with him? We don't get him early on in the game, so she never has any direct interaction with him. And she lives in 7th Heaven with the others. I'm wondering if she even knows him! Why would she hide herself behind him?
They've probably met or at the very least knows who he is, and he obviously just rescued them both, so there's no reason for her to not feel safe around him, really.
VincentxAerith now?
Vincent says he goes to the forgotten city often. Why? Kadaj's gang only got there like.. yesterday.
Since he's investigating the Shinra Company and their practices, and likely the cause of his own particular condition, it makes sense that he would spend time at the ruins of Cetra civilization. He's also probably something of a vagabond, and the forest and capital certainly suit his somber attitude, so it's not unlikely that he would rather be there than, say, Costa del Sol.
"Which is it? A Memory or us?"
This was something that bugged me for a while. Is she referring to the memory of the forgotten city and Aerith's resting place? I dunno.
She's basically just asking him if he's going to stay hung up on the past or if he'll move on and return to those who care about him and need him. He of course ultimately gets his priorities in order and moves on, coming to terms with the deaths of his friends and relegating Sephiroth to the status of "just a memory".