[1] The show centres on Dr. Helen Magnus, a 157-year-old teratologist, and her team of experts who run the Sanctuary, an organization that seeks out extraordinarily powerful creatures and people, known as Abnormals, and tries to help and to learn from them while also having to contain the more dangerous ones.

Sanctuary follows the exploits of Dr. Helen Magnus (Amanda Tapping) and her quest to protect various cryptids, legends, and abnormal animals/people with certain extraordinary powers and abilities (which most people would consider "monsters").

She is initially aided in her quest by her reluctant protégé Will Zimmerman (Robin Dunne); her intrepid, if somewhat reckless, daughter Ashley (Emilie Ullerup); the talkative geek and lycanthrope Henry Foss (Ryan Robbins), a computer and security expert; and her taciturn, Homo heidelbergensis-like assistant, played by Christopher Heyerdahl (whose character is unnamed, but listed as "Bigfoot" in the show's credits).

Helen was a member of a group of experimental scientists known as "The Five", which also included Nikola Tesla (Jonathon Young), Nigel Griffin, Dr. James Watson (Peter Wingfield), and Magnus' lover John Druitt (Heyerdahl again), who wanted to push the boundaries of their understanding of the physical world through unconventional means.

After the injection, they each developed Abnormal traits: Magnus experienced drastically slowed aging, and longevity with no clear limit; Nigel Griffin acquired the power to become invisible at will; Dr. James Watson's intellect was tremendously heightened; Nikola Tesla underwent transformation into a vampire, with the additional power of electrical manipulation; John Druitt developed longevity and the ability to teleport through time and space, but, already unstable and soon possessed by a malevolent energy creature (explained Season 2 Episode 11), he was driven to give in to his dark impulses, and becomes Jack the Ripper.

During the first-season finale, "Revelations", they test a small amount of a biological weapon named Lazarus that causes all types of Abnormals to become extremely violent, attacking anyone nearby and then dying painfully.

At the end of the second season and beginning of the third, a man named Edward Forsythe (Callum Blue) tries to take control of Bertha, and NY Sanctuary House Head Terrence Wexford (Paul McGillion) goes rogue trying to destroy her, even attempting to depose and kill Magnus.

Will visits the spirit plane via induced cardiac arrest, and while there he sees two other powerful beings in addition to Kali; encounters Helen's father, who gives Will a message for her; and then spontaneously returns to life with no brain damage after an unprecedented length of time.

The Sanctuary team speculate that the beings are avatars of Abnormals as powerful as Big Bertha, one of which may have been the source of the earthquake that stopped a destructive tidal wave started by Kali's wrath.

Meanwhile, Gregory Magnus's message leads the Sanctuary team to old birthday gifts that he had given to Helen years before, which in conjunction produce a tangible holographic map or miniature representing an unknown steampunk-style city.

The end results of his machinations were the destruction of Praxis, several armies of displaced Abnormals marching on the upper world, and his escape to the past to attempt to save his daughter, with Magnus hot on his heels.

She and her team manage to end the Abnormal assault on humanity without too much bloodshed, but still must contend with increasing persecution from the Special Counter-Insurgency Unit (SCIU), an anti-Abnormal agency.

This skepticism proves justified, since Caleb plans to release a substance that would bring out latent Abnormal traits in normal humans, effectively eradicating the species.

Now presumed dead, she is free to begin anew in an Edenic underground city based on the work of Buckminster Fuller and Albert Einstein, one last secret from her repeated century.

[58][59] USA Today reviewer Bill Keveney said that Amanda Tapping had reached her "comfort zone," and continued with further positive reaction to the TV series.

[60] Rick Bentley from McClatchy Newspapers commented Tapping's role as Dr. Helen Magnus was a way for the actress to make a name for herself outside of Stargate SG-1 as character Samantha Carter.

[61] Maureen Ryan of the Chicago Tribune described the show as "competent if not particularly innovative sci-fi," and said that the series might be of interest to fans of Tapping's earlier works.

[62] Mike Hale of The New York Times believed that the series does not have "the narrative force of Battlestar Galactica or the wit and creativity of Eureka," further stating "it's not an embarrassment for the channel, but it doesn't raise the stakes either.