Theory #5: The subject of the inception mission was actually Cobb (inception-within-an-inception).
Saito hiring Cobb to commit inception on Fischer was just a ploy. The actual subject of inception was actually Cobb, and Miles was the mastermind of the whole mission. This was plausible because Miles was the one who taught Cobb the skills of using dream technology, and he had enough experience to know that he could secretly tap on Cobb’s expertise to help him execute his mission.
Miles’ mission is this: To incept Cobb with the idea that he could be reunited with his real children.
Obviously saddened by the loss of Mal, Miles also understood Cobb’s tragic situation. It was a double whammy for Cobb, who lost his wife to insanity, and was forced to leave his children, possibly forever. Empathizing with Cobb, Miles sought to provide him with some measure of hope by creating this elaborate idea to incept him as he attempted to incept another person, in this case, Fischer. Ultimately, Miles wanted Cobb to be happy, and the only way was to introduce the idea that he could be reunited with his real children.
So Miles started with Saito, and told him to act as if he was the “subject” of an extraction mission by Cobb, who in turn was oblivious to the fact that he was being auditioned by Saito. Miles also enlisted the cooperation of Cobalt Engineering for this “audition sequence”. Later, Cobb found out he was being auditioned, and Saito seized the opportunity to persuade Cobb to take up a final mission – the inception of Fischer – and earn the chance to be reunited with his children back in the States, with all of his criminal charges wiped clean. This was the moment when Cobb was first introduced to the idea Miles had planned to incept in Cobb.
This theory is very interesting because two inceptions are happening simultaneously: (1) Miles on Cobb via Saito, and later, via Ariadne (I will explain her involvement in Theory #6), and (2) Saito on Fischer via Cobb. Since the idea had to be planted deep in Cobb’s mind without raising his suspicion, Miles had to rely on Cobb’s elaborate design of (2) to facilitate his plan of (1). (2) was what we saw from the film, whereas (1) was a subliminal process that slowly developed in Cobb’s mental faculties.
When Cobb was in the “building level” with Ariadne to find Fischer during the latter stages of the inception mission, he revealed to Mal (his subconscious projection) something he had been hiding from her – the commitment of inception by him on her. This action provided a kind of cathartic release for Cobb, who would now be able to return to his children after the mission without the spectre of Mal haunting him. This “exorcism of Mal’s ghost” was important for Cobb because Mal was the one single obstacle separating him from his children.
In the final sequence, we could see that inception had been completed on Cobb – he spun the top and left it alone; he did not bother about the outcome because he was sure that he had been reunited with his real children. And most importantly, he was happy about that.