1. You can give the Faceless the Cube (after retrieving it from Tchort's dead body) or fight them for it. If you fight them, Rham-Umbra (Six) will steal it from you and give it to them. After the Faceless have their Cube, Six will tell you that he is hunting a kin of his -- Hadrian Tanner (who has committed a war crime or something). You then investigate Tanner's room in SGS and find evidence that he was some imposter-robot all along. You then have the choice to join Six in hunting Tanner or become a co-leader of SGS. Both end the game. You aren't ever told what happens to Tanner should you choose to hunt him.
2. It's not well explained. He's part of the Occulus it seems, and one of the more powerful members (claiming to be more powerful than Tanner), and is probably a robot.
3. Tanner wanted the Cube to become more powerful than Six. That's why he sent you on all those missions investigating the Faceless and the Cube. He wanted you to find it and bring it back to him. That's also why Six was interested in finding the Cube -- to prevent Tanner from finding it or ideally find Tanner who was also searching for it. Anyways, Tanner started all the shit that happened by getting some one else (never revealed I don't think) to steal the Cube.
4. Never met him.
5. You may already know this since I don't know who's read the laptops: Dude (from Rail Crossing) is actually John Dyson -- a genius Biocorp scientist who was working in the DC. He was the leading expert on Psionics. In particular, he worked on Psionic Projections and the Monoliths (those crystals). It's never explained how he escaped the fallout of Biocorp's collapse and unfortunately you can't ask Dude questions when you return to upper Underrail
. Also the dialogue with IRIS, if you manage to Persuade her, is really cool and expertly done.
6. I don't know. I didn't help him.