Madara/Zetsu Connection and Theory
This theory is based on the stroy line of Kyoni in the anime "G Gundam". In this show a man named Kyojii and his father created a robotic suit, called the Dark Gundam, to help rebuild a destroyed earth. The suit operated by use of nanobotic cells call DG Cells. These cells later take over Kyoji after a crash landing on earth. With Kyoji in a weakened state and the programming altered in the Dark Gundam it took the chance to control Kyoji with the help of the DG Cells. With Kyoji has its power unit it started the deformation of Earth. Later Kyoji using the last of his free will created a clone and gave him the name Schwarz Bruder. This clone later helped Kyoji's younger brother destroy himself and the Dark Gundam.
Now lets substitute this with Madara and Zetsu. After the fight with the first Madara was extremely weakend and on the virge of dying. Along comes Zetsu who recognizes Madara and his chance to take control over him. Gaining control of this new found body he organizes Akatsuki to capture all tailed beasts and use Madara to achieve the Moon's Eye Plan. Also giving rise to Zetsu's double personality, the darker and more experienced half being Madara's mind. Later Zetsu creates a clone to help him with his plans, little does he know that Madara is actually in control of this body. Now Madara is trying to gain the power of the Juubi to reclaimed his lost body and his powers.
I just though of a second option. Zetsu absorbed Madara's weakened body which had a lot of dark chakra in it giving birth to Dark Zetsu. he then released Madara as a subordinate to achieve a plan of his. But little does he know that Madara has gained control of his mind and plans to get his powers back to take control of the world. Sorta like when Sasori's informant Kabuto acted as a double agent with Sasori and Orochimaru.