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It’s revealed in the third season, that the Northampton Farmhouse in this incarnation is known as the O’Neil Farmhouse. However, this house is actually the property of April’s Mother’s family, which meant her mother's maiden name was O’Neil. This in itself doesn’t mean anything as O’Neil is a fairly common surname, so it’s possible that both Kirby and his wife could have possibly shared the same last name. It’s also just as plausible that Kirby took Mrs. O’Neil’s surname as his when they were trying to protect April since his true surname could have been easier to trace.
It’s also never actually confirmed that Kirby is actually married to Mrs. O’Neil, so it could have been just as likely that Kirby and Mrs. O'Neil were never married. They could have had a common-law relationship at best our or they just could have played the roles of parents to April, all the while the two of them would maintain a platonic bond.
During buried secrets, Mrs. O’Neil does explain that April’s great-grandfather unknowingly built a house over a crashed Kraang ship. When he came across the ship the Kraang respond by experimenting on him and all his bloodline because they discovered his family had the one DNA strand needed to perfect their mutagen. Further news of Mrs. O’Neil is never revealed beyond this. All we have is April suspecting that perhaps her mother really is gone, and Leo tells her not to give up hope.
My friend and I surmised that perhaps Kirby may have been originally working with the Kraang before April was born. The following is a plausible explanation as to what could have been put into Kirby’s character if he was to be revealed to be an antagonist. Bear in mind much of this is essentually fanfiction, but it is a plausible explanation as to some of April's backstory from the 2012 series.
What my friend and I speculated as a probability was Kirby was invited to work at TCRI as a psychologist and be involved in an experiment that was being performed. Kurtzman does reveal in “Kraang Conspiracy” that the Kraang experimented on Mrs. O’Neil before April was born. So this moment would be where Kirby meets, Mrs. O’Neil who is there as an experiment...or rather as a vessel for a test tube baby that Kraang were creating. When April was born, the Kraang would have wanted Kirby to monitor her physical and mental development as that would be key to their plans.
Kirby goes along with everything he’s told to do with little question as to what the Kraang are planning. He is just eager to prove himself in this experiment so he can advance his career. At some point, Mrs. O’Neil informs him that the Kraang intends to use April as a living weapon that would destroy the Earth. At first, Kirby doesn’t know how to believe her, even when Mrs. O’Neil explains that her family had the DNA strand the Kraang needed to perfect their mutagen and April was going to be the catalyst to unleash it. After some thought and explorations of his own, he begins to wonder why he was really studying this child for the Kraang and why she was created. One day he catches, Mrs. O’Neil trying to escape with April. She tells him she wouldn’t let the Kraang use an innocent child for their own ends. Knowing he was risking a lot Kirby helps them escape. He also forges a new identity for himself taking on the surname of O’Neil with the hope that it would be harder for them to be traced.
The two of them raise April as their child. When April begins school, Kirby falsifies her medical information so there isn’t anything the Kraang could trace to them. Unfortunately for April, she finds difficulty in making friends because her awakening sensitivity would cause people to become uncomfortable around her or see her as weird. These psychic episodes also force April and her parents to move frequently so the Kraang won’t discover where they are hiding. During summers, the three of them would stay at the O’Neil farmhouse since it was in the middle of nowhere and it was the one place April could have a relatively normal life.
While Kirby has been going along with protecting April and had developed paternal feelings for her. He hasn’t completely bought the story that she is meant to be a living weapon for the Kraang. So he still maintains correspondence with them about her development. Mrs. O’Neil eventually learns that Kirby and has been communicating with the Kraang about April and that leads into an argument between them. Kirby insists that he wants to protect April, but his job was to monitor her development. Mrs. O’Neil, on the other hand, loses all trust for Kirby and plans to leave with April as soon as she is asleep.
Unfortunately for Kirby, the Kraang had been tracing his correspondence so they could obtain the then six-year-old April for themselves. Realizing they have been discovered Kirby and Mrs. O’Neil carry April to Kirby’s van. In a desperate act to protect her daughter, Mrs. O’Neil sacrifices herself to the Kraang so Kirby and April could escape. She is subsequently interrogated and tortured over where Kirby has taken April, but she doesn’t offer any satisfactory answers. While her ultimate fate wasn’t revealed in the show, the showrunners did explain after the series finale that April’s mother was indeed killed when she was recaptured. So ultimately the Kraang kill Mrs. O’Neil after they create a clone of her that was programmed to capture April and bring her to the Kraang. However, this clone was too difficult to control so the Kraang put her in frozen stasis.
Meanwhile, In New York City, April wakes up and asks Kirby where her mother was. Dr. O’Neil just tells her that her mother could no longer be with them. In the city, Kirby is able to set up a home for them with some help from his sister. He makes a cover story that he secretly eloped with someone and his wife had passed away recently.
Ten years later Kirby and April are spending the evening together, as they are returning home a van pulls up and some Kraang Norman bots accost them.
The Turtles who are out experiencing the surface for the first time see the abduction taking place and interfere with it. Ultimately, they fail in preventing the capture of the father and daughter. The two of them are put in a Kraang detention center until they could be transferred to another location. The Turtles arrive to save them, in the end, Donnie succeeds in only rescuing April while the Kraang continues on with Kirby as their prisoner.
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