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Agent Johnson was a British government operative tasked with investigating, and later assassinating, the members of Torchwood 3. Her primary motivation was to "protect the state", even if it required her to commit cold-blooded murder.
Johnson placed Rupesh Patanjali in the field to masquerade as a potential new member for Torchwood. After months of perfect infiltration, the plan was abandoned when, following the reappearance of the 456, she received orders from John Frobisher to terminate Captain Jack Harkness. Under Johnson's orders, Patanjali lured in Harkness and shot him. After confirming that Harkness did indeed recover from the seemingly fatal wound, Johnson had a bomb surgically placed in his abdomen, to destroy the Hub and sever Harkness's theoretical connection to the Rift, thinking it might be the key to his immortality. Deciding that Patanjali, having blown his cover, now was a security risk, she cold-bloodedly shot him in the back and had his corpse placed next to Harkness. (TV: Children of Earth: Day One)
After the bomb inside Harkness' stomach detonated, destroying the Torchwood Hub, Johnson positioned a team at Cardiff Bay to eliminate any survivors. They failed to catch Gwen Cooper and Ianto Jones, who made their separate escapes. She and her men coerced PC Andy Davidson into leading them to Gwen's home, who again eluded capture, shooting Johnson's vehicle's tires out. The next morning Johnson supervised the search for Jack's body and when remains were found, she ordered them sealed within a remote military compound.
When Jack's body reassembled and regenerated, Johnson had him encased in cement to keep him contained. However, Gwen, Rhys, and Ianto infiltrated the base and smashed Jack out of the cell with a fork-lift truck. Johnson and her men pursued the group, but were cut off in their pursuit by an exploding lorry Gwen and Rhys placed in the middle of the road. She phoned Mr Frobisher and apologised for their failure. (TV: Children of Earth: Day Two)
The next day Johnson's team located Alice Carter by tracing her phone call to the authorities asking after Jack. Investigating her mysterious background, Johnson's team determined that Alice was Jack's daughter. Johnson led the team that stormed Alice's home and cornered her in an alley as she made her escape with her son, Steven. (TV: Children of Earth: Day Three)
Johnson grew agitated as she found herself kept increasingly out-of-the-loop. Nonetheless, she continued to pursue the Torchwood team. She led the strike force that confronted Gwen at the abandoned Torchwood One holding facility the team had been using as their temporary base.
She was forced to stand down when Gwen revealed that Torchwood had blackmailed Johnson's superiors in the government. (TV: Children of Earth: Day Four)
After her encounter with Gwen Cooper and her realisation of what the government was doing, Johnson had a change of heart and helped Torchwood's efforts. She released Alice and protected her son (occupying his time by having some of her team play football with him), and broke Jack out of prison. She provided him with equipment needed — as well as getting Dekker — to analyse the 456's signature wave frequency. With these assets, Jack defeated the 456, sacrificing his own grandson. Johnson was visibly upset by Steven's sacrifice. (TV: Children of Earth: Day Five)
Personality
Johnson believed "the end justifies the means". During the 456 crisis, she committed murder at least once without any hesitation and attempted to orchestrate the killing of Harkness, Cooper and Jones. (TV: Children of Earth: Day One) She also shot a man in the leg simply because she was irritated with him for saying that it was impossible to defeat the 456. (TV: Children of Earth: Day Four)
Johnson initially exhibited a suitably cold-blooded personality, although she appeared to enter into a respectful relationship with Harkness' daughter, Alice Carter, to the point where she agreed to keep from Steven the secret that Jack was his grandfather, not his uncle. (TV: Children of Earth: Day Four)
Johnson was willing to sacrifice Steven to save the other children, declaring it to be "one for millions". Despite this she was genuinely horrified by the brutality of Steven's death and even shed a tear as she watched him dying. Despite her merciless, cold blooded personality, Johnson was not entirely heartless. (TV: Children of Earth: Day Five)