Cool things we learned this chapter:
1) Madara may have had some form of eternal life with hashirama's power, but he did not have eternal youth. Also, he was tethered to the Gedo Mazo to stay alive, and could not leave his little fort without dieing.
2) Madara definitely gave his eyes to Nagato, and replaced his left eye with another stolen sharingan
3) Obito's Kamui power activated, he phased through the rock, and fell down to Madara's underground chamber. From there, Madara used Zetsu slime to heal him. (Obito did not immediately become evil and seek out Madara. Madara did not intentionally search for, find and save Obito. It was a chance meeting).
4) Obito is, at least at first, unwilling to help Madara and did want to return to the leaf village (but was unable because he too was limited in range and needed to stay close to the source of the zetsu slime)
New Questions that we have to be answered:
1) How did Madara stay in contact with Nagato, and therefore maintain control over Akatsuki during this time?
2) Would Madara have died if Nagato had summoned the Gedo Mazo statue away from Madara's hideout? Is that why Akatsuki didn't capture any Bijuu for the first few years of its operations, because the statue could not be used to seal the tailed beasts if Madara was attached to it?
2a) Is that what the "Immortal" Madara chose to die, so that Akatsuki could start collecting and sealing the tailed beasts?
2b) Did Nagato know that he was supposed to resurrect Madara at the chosen time? If not, what was Madara's plan to get resurrected?
2c) Was Madara's plan for Nagato to resurrect him, and then steal his old eyes back from Nagato in order to use the final technique? How would an elderly Madara without his EMS/Rinnegan eyes have possibly been able to defeat Nagato and steal the eyes back for himself?
2d) Why would Nagato have ever agreed to resurrect Madara when Nagato's plan (use the tailed beasts as a weapon to end war) didn't require Madara's help?
2e) Was Madara tethered to the Gedo Mazo when Nagato summoned it to fight Danzo/Hanzo? If so, why didn't Madara die then? If not, why did he ever need to be tethered to it?
2f) Why would Nagato agree to use the Gedo Mazo to keep Madara alive artificially? Once Pain was the leader of Akatsuki with his own goals and motivations, why would he choose to keep a weakened, elderly Madara alive?
2g) Why did Pain think that Obito was Madara, if he knew the real Madara was a weak elderly man tied to the Gedo Mazo to keep himself alive? Did Obito just appear one day with the mask on and say "I'm Madara, I got younger!"? Wouldn't Pain have been suspicious about that?
3) Obito seems like he doesn't want to join Madara, and tries to escape. So how does he turn from that into Tobi who is a psychopath
who follows Madara's mission?
4) How was Obito able to leave the chamber eventually, without his Hashirama/Zetsu slime dieing as Madara suggested?
4a) Why didn't Madara untether himself from the Gedo and leave his chamber, if Obito was able to do this supposedly impossible thing?
4b) Is this the origin of Zetsu, the black half stabilizing the white half and allowing it to leave the chamber?
4c) And if so, how is it that white Zetsu is able to separate from the black half without dieing?
So we did learn a few cool new things but on the balance we have a lot more questions that need to be answered, where the answers are not obvious.
Some answers to your questions are answerable (not all though)... wait while I cast my genjutsu on u to answer some (keep looing at d dots........ ...............................

U_U................... ........... (notice where d spaces are? gd boy, those are plot holes the rest of the dots are common reasoning)
1) Madara set up akatsuki and Nagato and Yahiko were running it first as a war organisation until Danzo and Hanzo F'd them up... Then Madara told Obito everything he has planned and set up. After training Obito, he (Obito later came back in pretence as Madara and took over akatsuki again) and then started pulling the strings the way Madara had instructed him to, in order to guide the organisation to help his Moon eye plan
2) No that is just lame, Madara later died... and
note that it is the
Stem of hashirama cells (the translation is wrong) that Madara is connected to in order to help him live longer (he was tapping into the long life of the senju clan through the cells)... Nagato summoned Gedo Mazo after he matured and trained himself to master the rennigan more, and he needed time to use it (u cant just summon mazo without knowing its full use and how to use it and just start sucking Bijuus), btw he needed the other strong akatsuki members to assemble/gather and have strong bases to use it to suck bijuus because it needed concentration and a lot of chakra to do so.
2a) No I have explained it above in answer 2
2b) Nagato might have or might not have known that he was meant to resurrect Madara, but after training Obito and telling him all his plans in details through the sharingan, Obito became stronger and assumed Madara's position as the akatsuki leader whilst pretending to be Madara, and he started guiding the organisation and manipulating Nagato... He was later meant to manipulate Nagato when the time was right to resurrect Madara (may be when nagato was strong enough to use the chakra from all the bijuus to cast the resurrection jutsu without dying)
2c) Obviously, if Nagato resurrects him, he wouldn't be in the old state, it would be his prime because nagato's 7th part has power over life and death
2d) That is what he must have been allowed to think, until Tobi came back and started pulling the strings for akatsuki again... when the time is right he will manipulate him or psyche him to resurrect Madara for a new plan.
2e) Madara was connected to Hashirama stem cell not Gedo as the translation led us to think... btw Madara being connected to the cells didnt mean that he couldnt die, it just allowed him to access longer life force that the senju clan has, so he can stay alive and age longer.
2f) Pain (Nagato was only the leader till Tobi took control again and started giving orders... e.g He was even ordered by Tobi to go and get 9tails... so clearly he was no longer in control of akatsuki, instead Tobi was now d string master.
2g) In the timeline of the story, Nagato was given the eye at a young age (probably during 2nd war, where Jiraya and d rest were named the 3 sennins; after which he trained Nagato and his mates for 3 years, then went back to Konoha and trained Minato later at age 12 since Nagato was older than Minato and Obito who is Minato's student during the 3rd war) so he clearly doesnt know Madara's real face (I'm speculating this)... And another speculation may be that Madara was wearing Mask after he left the village and went into hideout, so Obito started using the same mask.
3) Obito clearly didnt want to join Madara, but after he must have healed up, he went back and noticed that Rin (his dream) was dead... he began to realise what Madara had told him that the world was full of pain. So with that in mind, he came back and accepted Madara's offer as his new dream/goal, since he had no goal of protecting anyone anymore because the one he wanted to protect is dead.
4) By now u should have known that Hashirama cells would have healed him remarkably (if u look at the hand where naruto hit him with rasengan, it has healed), so he was now able to move and probably found a way out or practised with his sharingan on space time jutsu and used it to get out to d village and noticed Rin was dead.
4a) Madara told Obito there was no way out because he didnt want him to leave, remember he is trying to convince Obito to stay because he needed his help, why would he then tell him the way out.
Think of this: If there wasn't any way out, how did Madara get in?
a way in = a way out
4b) Yes Zetsu was formed from Hashirama stem cell.... as u can see in chapter 602, the human-like creature from the stem cells resembled Zetsu
4c) I dont know about the full details of white and black Zetsu formation and combination...
Hope my explanation helped a lil bit, it might not be 100% accurate though but from my research I can tell u I am sure of these things :ice:

xd