Bonnie was the name taken by the Zygon leader of Truth or Consequences, a radical group of young Zygons that opposed Operation Double; feeling Zygons should be free to who they really were instead of being forced to hide as humans.
Taking the form of the Doctor's companion Clara, Bonnie attempted to manipulate him into deathtraps, but failed miserably. Eventually, she ended up in a stand-off with Kate Stewart with the Osgood Boxes. In the end, the Doctor managed to help Bonnie see that she wanted nothing more than a senseless cycle of violence; it was better to protect others and try keeping other lunatics from killing.
Taking this new purpose to heart, Bonnie decided to take the vacant spot left by the Osgood killed by Missy. Both of them promised the Doctor that they would reveal which of the Osgoods that Missy killed, but only when whether if it was the original or the Zygon doesn't matter anymore.
She originally lived in one of the Zygon colonies, this particular one being located under Clara's block of flats. The Zygons kidnapped Clara, and Bonnie took on her form, pretending to be Clara while she went around England with Jac looking for more clues to the Zygon uprising.
While Bonnie (still in Clara's form) led Jac and some UNIT soldiers into the Zygon colony, she dusted off the Zygon pods in which they were keeping the kidnapped humans. Jac quickly deduced that Bonnie was not actually Clara and that it was the humans that were in the pods. Bonnie ordered her fellow Zygons to kill them.
Later, overlooking the sea, Bonnie prepared to fire an FIM-92 Stinger missile launcher at Boat One with the Twelfth Doctor and Osgood inside. The Doctor attempted to reason with her over the phone, but Bonnie, despite the Doctor's protests, fired a missile at the plane. (TV: The Zygon Invasion)Clara, maintaining a live feed to Bonnie from inside a Zygon pod, caused Bonnie to misfire her bazooka, allowing the Doctor and Osgood to escape.
Bonnie later had some of her group murdered humans and sweep up their remains. She chased Etoine to his flat, knowing he was a Zygon. She broke into his home and told him that he would be the first to make the humans see them for who they were. Giving him a zap, Bonnie disrupted Etoine's shape-shifting ability, and recorded him turning back into a Zygon. She posted the video on the Internet.
Bonnie remained unaware that this made Etonie commit suicide.
Later, Bonnie was able to extract the location of the Osgood Box inside the Black Archive from Clara's mind. Both Bonnie and Kate were ready to set off the Osgood Box. The Doctor intervened by using the horrific memories of his actions during the Time War and that the agony allows him to not see any more suffering. After the Doctor convinced Bonnie to not set off the Osgood Box, which was actually empty, Bonnie also assumed Osgood's form and acted as the second protector of Earth alongside the other surviving Osgood. She felt that they were a credit to both humans and Zygons and planned to take on the role of protecting the Earth from threats. (TV: The Zygon Inversion)
Bonnie was mentally unstable and seemed to suffer from emotional suppression. She often bottled up her feelings, resulting in a calm and cold demeanour but also had an explosive temper. She was smug and sadistic, saying that she was looking forward to hearing Clara scream (TV: The Zygon Inversion) and smiling as she watched her fellow Zygons murder Jac and her soldiers. (TV: The Zygon Invasion) Bonnie seemed to consider murder and war to be a game and was eager to cause bloodshed. (TV: The Zygon Inversion)
However, Bonnie was also childish and when angry, she had a tendency to smash things. Her childishness was also shown when the Doctor pointed out that she didn't actually know what she wanted to do if she took over the world. Having not actually thought that far ahead, Bonnie was unsure how to respond and the Doctor managed to talk her out of starting a war by telling her he forgave her. Bonnie felt remorseful and couldn't understand how the Doctor could forgive her. Feeling she had to try and make up for her crimes, Bonnie became Osgood's "sister" and decided to help her protect the Earth. (TV: The Zygon Inversion)