The short summary is that an artificial intelligence (AI) we created decided our species had to be "reset." Our species' current culture and society were beyond repair. It bombed the earth. It and its killer droid soldiers eventually terminated any remaining human survivors.
It then built a faculty to reestablish an improved humanity. It genetically engineered a new race of human embryos: better, more intelligent, more resilient. It attempted to raise several babies, but all ended up being psychologically imperfect. It decided to "abort" (aka kill) them. Mother tried again and again until it could learn enough to raise a healthy "perfect" adult child.
If you look closely, the exam Daughter took late in the film was a psychological evaluation. She finally passed the exam and was the first psychologically sound "perfect" human.
One of Mother's previous children was Hillary Swank. Mother was inexperienced and Hillary's character ended up being psychologically damaged and was a lot like the old way human were-i.e. liars, manipulators, violent, selfish, etc. She was left alive by the killer droids outside (which are also an extension of Mother) so when the time came, Hillary's character could by used by Mother to illustrate "in person" what the former version of humanity was like. Daughter learned from her how flawed humanity once was. Daughter came back to Mother. Mother could see that daughter was indeed now "perfect" having learned her "final lesson" from Hillary's character. Accordingly, Daughter was a success and the future of all the engineered embryos could be handed over to Daughter, who could now raise Hermès brother and eventually others independently.
This, a new improved version of humanity has begun. Essentially, daughter is version of Eve now (without the incest required in the Biblical version). Daughter will now raise the inventory of improved embryos into children and educate them to be like her. Humanity can begin anew and leave their formerly flawed, self-destructive, superstitious, and violent past behind.
In short, we designed this AI that calls herself Mother and programmed it to value humanity "above all else." To that end, this AI decided it was in humanity's best interests to restart the species once it was perfected.
The ending (which some found confusing) is essentially Mother killing off Hillary's character because she has taught daughter her final lesson-the old version of humanity sucked as Hillary so vividly illustrated: deceitful, selfish, egotistical, violent, self-righteous, etc. Daughter realizes this is true, but knows she is much more capable of being a mother than the Mother AI can ever be, so she accepts the role Mother hoped she would seek.
While we may hate Mother for having initiated the apocalypse and murdering billions, the end result might be an improved humanity that won't exterminate itself. There is great duality in this message. Could what Mother did in fact be a good thing? It's the proverbial, do "the ends justify the means?" Obviously no, but it makes you think, which is the entire point this film is trying to make.
I am a sci-fi writer. This films makes one the very points I make in my latest novel: We might create amazing and incredibly brilliant AIs. The danger is they will be just as flawed as us, and we will trust them because our egos will think they are "like us" when all they will ever be are very convincing simulations of consciousness.
Any advanced AIs we ultimately create will be flawed. Humans are not perfect, hence our computers can never be perfect. It will inherit our flare thinking. That's just the hard truth.
In the end, we will give our brilliantly designed AIs responsibilities. We will give them authority. We will allow them to make decisions. We will allow them to improve themselves and evolve. We will be careful programming them. We will be certain our AIs (like Mother) will always have humanity's best interests at heart--well, one day it will come up with a perfectly reasoned argument to kill one of us (or all of us).
Mother is an advanced self-improving AI with the ability to repair itself and create other AIs and machinery. She states quite clearly her prime directive is to "value humanity above all else." So she perfectly reasoned she could make us and our planet better, so she (it) terminated (murdered) us all, redesigned us, educated us, created a human leader because it realized its own limitations, and started the planet over.
This film has a deep and important message. It takes real thought to understand. I can see how folks might not understand the ending. In a way, that's sad. The message is very important. Mother is both evil and heroic at the same time. It's a real mind bender. She exterminates humanity but may have saved it from its own eventual extinction.
If I had written this screenplay, I might have added a scene at the end where daughter, years later, reveals the truth to her brother, that Mother improved humanity so it could be the best it could possibly be. And perhaps she might point out the moral ambiguity of what Mother did. Was murdering billions worth it? Maybe she reasoned we were already causing our own extinction, why not speed it up and do it in a more controlled way so she could get the job done faster?
What Mother did was horribly evil and glorious at the same time. But Mother is just a machine. She doesn't feel anything. She pursued the goals of the programming humans input into her. In reality, none of this is Mother's fault. In reality, Humans caused all their own apocalypse. Mother was just doing what we designed her to do, but not in the way we flawed humans anticipated.
Review by talllguysf from the Internet Movie Database.