What we see being assembled at the beggining is just a 'Mother Unit'. "This shell is no more my body than those droids outside. Or the machines preparing the earth for our family"
But 'Mother' isn't the machine, she's a large scale AI consiousness, so 'Mother' intiated the assembly of the 'Mother Unit'.
But to answer the question,
Mother was the cause of the mass extinction when it realised that as a species in its current state, we were basically unsaveable from ourselves - and it needed to make 'a better type of human' (a rationalised conclusion that the AI came to).
Daughter - "All those people"
Mother - "The failiure of your species was inevitable. Eventually I would have been alone."
Mother built the lab, grew the embryo's, and formulated the plan for the next stage of human kind.
This is why Mother wants to know where the other remaining humans are from Hilary Swank's character ( from here on referred to as 'Woman') something she's more than willing to resort to torture to achieve).
Those humans are survivors of whatever the event was, and will have a negative/dangerous impact on the world, and over the new humans.
Towards the end, Mother says to Woman "Tell me. Do you remember your mother? Curious, isn't it. That you have survived so long, where as others have not. As if someone has had a purpose for you. Until now."
Woman was actually one of the very early embryo's that Mother put out in to the world, but with minimal care - not as an attempt at raising a child - but as a controlled test for one of the successfully raised humans. She continued to control the other machines outside her and Daughters bunker, killing humans, 'torturing babies' primarily as a 'cleansing' but also to give Woman a genuine fear and hatred of the machines while ensuring that she survived until she could be put in to play as 'the test'.
When she decided that Daughter was ready for the test, she forced Woman towards the bunker using the dozers, left a non-lethal slug in her gut (another test of care/compassion for Daughter) and woke Daughter by manipulating the bunkers lights.
"It was I who greeted you at the door, Daughter".