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After returning from her time with the Brane of Extraordinary Women, Alex enlists her parents' help in applying the lessons she learned: planning her schedule out, keeping her stories straight, choosing a costume that will effectively disguise her identity, and selecting the Code Name "Terawatt". She also reaches out to the local version of Willow Rosenberg, a genius computer programmer, whom she is able to recruit as tech support.
Danielle Atron, Alex's arch-nemesis, is suspicious of "Terawatt", but the alterations included in her disguise convince Danielle that she isn't Alex. Danielle continues sending super-criminals to Paradise Valley, though, to test Terawatt's abilities and try to bring her down.
After Terawatt successfully fights off Victor Cready, an out-of-control flying pyrokinetic, the US military notices her actions, and Colonel Jack O'Neill persuades her to work with his division, the Superpower Research Initiative, within the Department of Homeland Security. She assists them in investigating a suspected poltergeist, which turns out to be a number of teenage boys with invisibility; they are able to recruit Grover Dunn, and arrest the others. Also, based on her alternate universe information, the SRI decides not to hire Mad Scientist Maggie Walsh; Walsh is angry and promises revenge.
Danielle develops a suspicion that Alex knows who Terawatt is, and empowers Joelle Baker, Alex's former school bully, giving her Super-Strength, Super-Toughness, and blue skin; Jo calls herself Azure Crush and comes after Alex for revenge. Terawatt is able to incapacitate her and administer GC-161 antidote, but Danielle meanwhile kidnaps Alex's parents; they break out by using smuggled GC-161 to temporarily give themselves unstable superpowers, while Terawatt and the SRI subdue and capture Danielle, who has given herself GC-161 superpowers but has less experience in using them. Unfortunately, Danielle's antidote wears off after a few weeks, and she breaks out of prison and disappears.
Terawatt then becomes involved in tracking down a genetically engineered girl named Hanna Heller, with moderately above-human strength and speed, who was rescued from experimentation and raised away from civilisation. Hanna is injured and unwell when found, but recovers and is placed in Dr Janet Fraiser's care. In the process, Terawatt also makes contact with her universe's version of Hermione Granger, choosing Hermione as her liaison to the EU.
After several quiet weeks, the SRI team, now including Hanna as "Action Girl", has to deal with a mutated giant tarantula the size of a building (and its hundreds of babies), then a blob monster that devours anything organic it touches, both courtesy of experiments by Maggie Walsh, who is working on behalf of the mysterious Collective. They also investigate a monster attack in Tromaville that turns out to be a vigilante attacking the corrupt town leadership; the team intervenes to have the situation properly resolved, but Jack decides against recruiting him.
Willow takes Alex to Comic-Con, where Terawatt takes the opportunity to judge the Terawatt impersonators. They also stop an illusionist from robbing an armored car. General Hammond, Jack's superior, later meets Willow and arranges to hire her to upgrade the DHS computer security.
The danger level then escalates with news that China has nuked one of its own cities, Lanzhou, to destroy an unspecified threat, and Hermione alerts Terawatt to the existence of silicate-based indestructible predatory monsters in several locations around the world (again courtesy of Maggie Walsh), which are narrowly contained with significant loss of life. Shortly afterward, Israel nukes Beirut at Lebanon's request, to everyone's astonishment. The cause of the nukes is not revealed, but China does confirm that it wasn't silicate monsters, and reports from Beirut indicate a rise in local violence just beforehand.
After hearing incident reports from New York, Terawatt makes contact with up-and-coming Bruce Paine/Batman, who is suspicious of her, and prefers to continue working alone, but exchanges limited help. They are able to arrest Bane and Poison Ivy in the process.
A few weeks later, the SRI team investigates a destroyed research lab and rescues eight-year-old Charlie McGee, a tremendously powerful pyrokinetic who was kidnapped and illegally studied by a rogue government agency until she broke out. Alex persuades her parents to take "Shar" in, on the condition that Alex assumes most of the responsibility for her care and schedule (since her parents work full time).
Danielle Atron breaks Jo Baker and Victor Cready out of prison and locks them away to wait for their antidote to wear off, hoping that they'll attack Terawatt again, as a distraction from her traveling to join the Collective. However, Victor is just desperate for more antidote, turning himself in at the first opportunity, and Azure Crush ends up using her enhanced body for fame and fortune as a nude centrefold instead of returning to wanton destruction. "Az" also gives Terawatt some assistance in dealing with giant mutated clams that have been devouring people on a beach, as she feels a kinship to the homeless people who were a large proportion of the victims. Nonetheless, Danielle reaches the Collective unhindered and starts working for them to develop and improve GC-161. She later sends several supercriminals to attack Azure Crush for her inaction, but Terawatt intervenes in time to rescue her, further thawing Jo's attitude.
Terawatt visits the White House to be deputised by the president, but is attacked on the way, in an attempt to replace her with an impostor, Clare Tobias; however, she is able to subdue her attacker, and Colonel O'Neill sees through Clare's disguise. Clare is arrested but later escapes.
The Collective's next attack takes the form of a giant dinosaur monster, dubbed Gojira, which attacks Japan and is able to incapacitate Terawatt. However, Shar rescues her, then runs away without permission to help fight Gojira; it takes her firepower, Terawatt's flight, and a new Japanese cryokinetic, Tsurara, to bring Gojira down.
Jack and Willow become engaged, shortly before a branch of the Collective sends emails to various individuals around the world, informing them that they are "Breslynn Orphans", the result of genetic experiments to produce enhanced humans — smarter, stronger, faster, more attractive, more driven to succeed — and inviting them to join the Collective. Willow is included, as are Jo Lupo, Riley Finn, and Sergeant Carlson of the SRI; all are distressed by the news, but Colonel O'Neill remains confident that they can be trusted. Clare Tobias, who tried to impersonate Terawatt, is also suspected to be an Orphan, as are Bruce Paine, Buffy Summers (a figure skater in this universe), and Selina Kyle (married to a billionaire, and likely to be the source of a great deal of the Collective's wealth).
After a tip-off from another elite team, STARS, the SRI team investigates a mansion and destroys an outbreak of monsters resulting from a transformation virus developed by Umbrella Corp. Sergeant Finn is infected, but a cure is developed early enough to save him, and he's left with only an improved Healing Factor. Most of STARS is killed, but Jill Valentine, another Orphan, joins up with the SRI. Interludes show that this project comes from a different Collective bloc, and that they are competing as well as cooperating.
Alex then intercepts and captures Clare Tobias attempting to expose a computing conference to a synthetic prion that damages brain pathways to turn people into killing machines — the suspected cause of Lanzhou and Beirut. However, the investigation of the prion is interrupted by the news that North Korea has exposed hundreds of thousands of soldiers to mutagens. Although most soldiers died, some of them developed dangerous powers, which they use to attack South Korea; the SRI team — with Azure Crush pitching in — helps to fight them off.
Samantha Carter, on a space shuttle in orbit, then gets into a crisis when a sample of organic material from a comet turns out to be a fungus that eats any organic matter it touches. The NID attacks the station and steals samples of the fungus, but Terawatt is able to assist Carter in eliminating the remainder. Clare Tobias is also ordered by Walsh to get rid of the lifeform at any cost, as it is too dangerous even for the Collective, and helps to destroy the NID's samples.
The FBI then finds a lead on the source manufacturing the hate plague, but when they move in, a plane escapes with some of the contaminant, and a town is exposed. The National Guard and SRI contain the situation, but with heavy casualties, as local residents and animals go mad and attack anyone they see. While Terawatt is helping, Maggie Walsh also springs a trap to capture, interrogate and kill her, but she narrowly escapes. In the process, Maggie reveals that the Collective's goal is to drastically reduce Earth's population so that the Orphans can have more resources to build a paradise from what's left.
Alex attends an EU liaison meeting as both "Lieutenant Annie Farrell", adjutant to now-General O'Neill, and Terawatt, and blocks a clumsy attempt to poison the attendees. While there, she also participates in investigating a group of psychic children in Midwich; the children trap them all in illusions of their worst nightmares, but are beaten back by a deadman-switched grenade, and finished with carpet bombing when the team doesn't make a scheduled check-in. Several SRI members are traumatised by what they saw.
Riley Finn contacts his wife, a doctor in Africa, for reassurance in the wake of his nightmare, and finds that she's been attacked and injured by a group of Orphans in the area. The SRI flies in to help, and in the process, makes contact with Eliza Thornberry, who can speak to animals. However, General O'Neill is captured by the Collective's India bloc, and gets in the middle of a fight between them and the Walsh bloc, which kills most of the Orphans on both sides before Terawatt and "Shaman" (Eliza) rescue him.
Sam Carter turns out to have gained a variety of telekinesis from the remains of the fungus in her, and is imprisoned by a military doctor, but O'Neill and Terawatt rescue and recruit her.
The primary Collective bloc then launches a full superpowered assault on India, and the India bloc retaliates with a nuclear strike and evacuation into space, intending to trigger a worldwide nuclear war and return years later to rule over the survivors. Terawatt, with help from local superhero Ayananta (who flies and shoots yellow beams), is able to blunt the primary bloc's invasion and disarm the one nuclear missile that the India bloc is able to fire, and their spacecraft turns out to have been sabotaged so that they will never return to Earth.
Alex graduates from high school as prom queen, wins a Pulitzer prize for her initial footage of Terawatt, and moves to an apartment for her study at Corcoran College. Her mentor, Frank West, learns her identity so that he can cover for her absences, and supervises when she's helping with the cleanup of Umbrella Corp. The team also intervenes at another school's prom, but is unable to save Carrie White, a very powerful telekinetic, who is mortally wounded by people afraid of her powers and does not trust Terawatt to help her. They do, however, meet "Ultraman", with super speed, strength, and flight.
During the summer, Alex takes a holiday to Paris with her aunt, and finds that an Orphan has released a mind-altering enhancement serum into the water supply, turning people into vicious killers with Super-Strength; she helps local forces, including Harry, Ron, and Hermione, to push back the attacking victims. Hermione is able to deduce her identity, but chooses to cover it up.
Tragedy then strikes when Alex, Shar and Hanna take a road trip before Willow's wedding. A Collective group's nanotech experiment escapes containment nearby and takes over Shar's body; Shar uses the remainder of her self-control to gather all the nanobots to herself and immolate them all in a nuclear-scale explosion. Alex is gutted by her death, for which she feels responsible, and attempts to retire from being Terawatt.
However, shortly after Jack and Willow's wedding, the Collective launches a wide-scale kidnapping of the remaining Orphans, including Willow, and they take Jack as well, who is revealed to be an earlier, beta test experiment. Bruce Paine successfully fights off his attackers, as does Buffy, and both contact the SRI afterward. From forensic evidence gathered by Bruce, the SRI is able to pinpoint the location of the Collective's remaining base, and gathers all available forces, including a reactivated Terawatt, Ayananta, Shaman, and even Victor Cready (working as a team with Tsurara) for a combined strike. In the resulting conflict, Jack and Willow are rescued, and Maggie Walsh is killed, along with most of the remaining Collective members, while Danielle Atron is split by GC-Divide, with only her "good" half surviving. Clare Tobias is revealed to have been a double agent under the direction of a different government agency, and assists in the takedown.
The epilogue shows Terawatt over 70 years later, widowed with grandchildren and having retired her Alex Mack identity, but still active and with her body not ageing normally.
