Absentia Season 1 finale, Episode 10, titled Original Sin, finally confirms who the real kidnapper of Emily was.
In the scene where Emily is inside a cabin or bunker, Emily confronts her kidnapper as the person speaks to her through a TV screen. The kidnapper recounts the childhood experiments at the orphanage. The person then removes the mask, and the kidnapper is revealed to be Laurie Colson, whose real name is Logan Brandt.
Therefore, this final ending reveal makes Laurie Colson aka Logan Brandt the main antagonist of the show. Read on to know more.
Who kidnapped Emily in Absentia?

The synopsis of Absentia season 1 finale episode 10 reads,
"Tommy makes a new discovery that puts a new light on the investigation. Emily's past faces the present when she finally meets her captor, and will be like a game of cat and mouse. When Nick gets hurt, Emily has to face several situations to save the ones she loves."
The synopsis itself states that Emily meets her kidnapper, and this happens via a TV screen where the kidnapper reveals her mask and turns out to be Logan Brandt, formerly known as Laurie Colson.
The suspense about the kidnapper is built when the masked person talks about Emily's past when she was in the orphanage. This surprises Emily, and she discovers that the kidnapper is none other than someone she was with in the orphanage. Emily and Logan were in the same orphanage and were selected for Dr Shen's horrific soldier conditioning experiments. Emily is supposed to be the test subject, but she swapped files with Logan, condemning Logan to six years of torture and brainwashing.
This way, Logan grew up into a killer who wanted to take her revenge on Emily. Eventually, Harlow and Laurie kidnapped Emily and tortured her for six years. Meanwhile, Logan also reinvented herself as Laurie, a journalist, and, along with Conrad Harlow, started to target and kill young women. She used to copy Shen's torture methods. These murders were staged so that Emily, missing and presumed dead, would later be framed.
After almost six years, Harlow then faked a confession that Emily had been found, but was mentally broken. Laurie then manipulated the investigation from within, subtly pushing Emily toward instability while presenting herself as a professional ally.
Therefore, we can say that Laurie emerges as the real architect behind the season 1 crimes.
In the finale episode of Absentia season 1, Laurie abducts Emily's son, leading to the climax

The plan culminated when Laurie abducted Flynn, Emily’s son. She wanted to provoke Emily to kill Alice, completing her transformation into a weapon. But Emily resisted despite being tortured physically and psychologically.
In the final confrontation in Absentia, Emily drowns Laurie and also uncovers the bodies of all the victims Harlow and Laurie had killed. Afterwards, FBI agents arrive at the cabin. Emily is taken into custody briefly, while the truth comes out in front of the world. Laurie and Harlow were identified as the serial killers behind all the murders.
Emily returns home to celebrate her son's birthday, but her psychological condition is not better. She sees an absurd vision of Harlow's body floating on the water's surface.