The storyline of this comic is fairly vague in spots, to the point where it almost seems open to interpretation. I recommend reading the original comic first, then coming back to this interpretation/explanation.
This comic prompts me to think about an aspect of the Matrix not brought out by the Matrix movies: if a pregnant woman is freed from the Matrix, what happens to her baby? After all, the pregnancy in the Matrix is a simulation. As Morpheus said, the human fields are places where "babies are no longer born - they are grown." If a baby is grown in a chamber of its own with little spider robots to nurture it, then who really is the baby's mother? Is it the human who simulated conceiving the baby in the Matrix, or is it the machines/Matrix system itself that "grew" the baby in the real world based on DNA specifications of the parents?
A woman (nameless in the comic) wakes up in the real world. She is right in the middle of the machines' human baby harvesting fields, with many spider robots crawling all over her. She gets frustrated that the robots don't realize she is awake, and one spider pokes her, apparently to wake her up. She squishes the spider in her hand.
An earpiece (not to mention the verbal exchanges she has with the operator) indicates that this is just part of a controlled simulation. She looks out into the field and says to herself that she is doing this not for Zion or the scientists, but for all the babies in the field, and especially for herself, as she looks at one specific baby in its red chamber. Presumably, this baby (or at least the baby this baby represents in the simulation) was her own in the Matrix until she was freed from the Matrix.
She unplugs the pink "womb" that the baby is inside and puts it into a sling (resembling what a woman looks like when she carries a real baby). One of the harvesting machines sees her and comes after her. She says, "Oh God! No!" and says she needs a way out of the simulation "now!", indicating the situation is out of control. The operator instructs her to head for the waste funnel, where they can meet her at the bottom. Presumably, this is a place she can exit from the simulation.
She jumps into the funnel with giant tentacles from the field machine following not too far behind. She loses grip of the bag on her way down, but she is able to grab it. Before getting to the bottom, the machine tentacles grab her in a way that seems to kill her with a loud "crunch". Her scream eventually turns "digital": "NOOOOO1010101...". The operator seems to think she's out and comments that he's not surprised the simulation failed, and that they need a male to do it next time. This implies that perhaps she shouldn't have unplugged the baby, and maybe she did it because she is unable to control her feelings about her baby, even if the baby is just a simulated one.
As he is about to unplug her, he realizes she did not make it to the bottom of the funnel. He says, "You bastard! I'm not giving up now!" Presumably, he's cursing at the machine that killed her. From there the scene jumps to a scene with her baby standing in a doorway saying, "...mama?" She wonders if it is the same bad dream she's had. The graphics of the comic in this scene indicate she's coming out of a binary digital world entering a non-digital one, so this scene seems to be some kind of afterlife or hallucination.
The comic ends with her hugging and saying comforting words to her baby, who is now a walking toddler. M1 shows a baby being transferred from a cocoon to a pod at about birth age, so this scene has to be a hallucination since the original baby she unplugged from the simulated baby field was still in its cocoon. The toddler is shown to have a headplug, meaning the toddler was born inside of the Matrix. Since she says "Mama's fine" while hugging him, this must be the baby she was pregnant with before she swallowed the red pill.
This comic leaves a few unanswered questions.
First, What exactly is Zion and its scientists hoping to accomplish with simulations like this one? To me, the most reasonable answer is the question of how to get babies out of the Matrix when their mother has been released. Even though babies should die if their mother takes a red pill and leaves the Matrix, machines might still be able to keep these babies alive and, once born, abandon the baby somewhere in the Matrix for it to be found and given to a foster home. If this isn't the purpose of the experiment, I don't know what the point would be of entering a simulation with the focus of retrieving a baby.
Also, if the main character failed in the simulation due to her inability to restrain her female impulses, then what exactly was her objective inside the simulation? Was it to simply identify which baby was the correct one, then leave?
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