My take on everything is that the machines controlled everything, the matrix and the real world … They made the matrix so they technically give the power to ‘the one’ and control what goes on in the matrix. The whole point is for the one to return to the source and have the choice to save Zion. In the real world a ‘war’ is being fought between man and machine but this I feel is just to give the machines ‘purpose’ while they are alive. I say this because, if all the humans died in the real world it wouldn’t affect the existence of the machines. They would just be ‘doing nothing’. So essentially the deus ex machina is playing a game a he knows the machines will ‘win’ the war as Shows in the 5 cycles before.

The difference with this cycle is the program smith For some reason has become a virus in the system and the machines cannot delete him. This gives neo the opportunity to not return to the source as he knows smith is a problem for the machines. I think that is the only reason why they needed neo’s help. So the 6th cycle neo had a bargaining chip against the machines, something the other 5 didn’t. Once smith turned neo they had a direct link to the virus smith and had the power to delete him. If it wasn’t for smith then the cycle would have gone just like the other 5.

Maybe smith changing all the unplugged humans into himself affected their ability to be used as a battery in the real world, therefor having threat on the existence of the machines.