Mandragora Helix

The Mandragora Helix was a Helix Intelligence, composed of helix energy (specifically called "Mandragora energy"), that existed as its own domain in "unchartered regions of the Time Vortex." (PROSE: Doctor Who and the Masque of Mandragora) Whether it was an individual or a hive mind is unclear.

Origins
The Mandragora Helix originated in the Dark Times, the Tenth Doctor commenting that it should never have been freed from its dimension. (PROSE: Beautiful Chaos) It may have been during this time that it gained knowledge of the Time Lords. (TV: The Masque of Mandragora)

Physical Appearance
The Mandragora Helix was a spiral of pure energy that radiated outward, able to draw things into it, even a TARDIS. The function of the spiraling energy was a complete mystery. Inside the Helix was a black void where sound echoed and a series of concentric crystal rings stayed suspended, but there was a "ground" where beings could walk. Balls of helix energy, which looked like sparking, irregularly-shaped red blobs, might bounce around in this void. (TV: The Masque of Mandragora)

Powers
The Mandragora Helix was an intelligent astral force capable of speech. It had a powerful psychic force that could easily infiltrate human minds, yet might be repelled by the mind concentrating on something. The Helix seemed to exist as Mandragora energy and portions of this might be separated from the Helix and still act independently. Mandragora energy was the "subthermal recombination of ionised plasma" that could float through the air and burn anything it touched. With humans, contact resulted in instant death and a blue crystalline growth on the skin. This energy could be spread out over things like stone (recreating ruined structures) or living beings. In humans, the energy took over their bodies, giving them a white appearance that bleached out their faces but also allowed them to fire bolts of energy from their fingertips. With this energy spread out over stones or humans, it became exhausted more quickly. It could only acquire more energy at certain times. When in this exhausted state, it could be absorbed through wire, with a ground like negative energy in magnetism.

The Helix could apparently travel through space but, in the case of Earth, could only reach the planet when the stars lined up in a certain order. This opportunity might come in five hundred year cycles. (TV: The Masque of Mandragora) Mandragora was an astral force that based its powers on astrology, and while some people might not believe in it, this didn't stop Mandragora from using things like the Zodiac as power. (PROSE: Beautiful Chaos)

Pre-history
Mandragora had at least heard of the Time Lords and also knew of humans. It was worried that Man, if unchecked, would not be contained in his own galaxy, ultimately entering Mandragora's domain and becoming a rival in the universe. (TV: The Masque of Mandragora)

15th century
Having slipped inside the Doctor's TARDIS from its domain, the Helix travelled to late 15th century San Martino in Italy. It manipulated the Brotherhood of Demnos into believing it was the god and eventually possessed the leader, Hieronymous, chosen because he was the Duke's astronomer. Mandragora promised him he would be the Earth's supreme ruler. It took over the cult's members and planned to destroy several scientists who had been gathered so that Earth would be prevented from having the Renaissance. As the helix energy was exhausted, the Fourth Doctor was able to completely destroy it. (TV: The Masque of Mandragora)

19th century
A force believed to be the Helix manifested in 1863 China, where an earlier Doctor confronted it without fully understanding it, as the Helix had encountered him in a later point in history, yet an earlier point in the Doctor's personal timeline. (PROSE: The Eleventh Tiger)

20th century
As the Fourth Doctor had earlier predicted, the Mandragora Helix re-appeared in 1990s London, this time exploiting the use of an illegal drug called Mandrake (another name for Mandragora). The Seventh Doctor and Ace, with the help of UNIT and Captain Muriel Frost in particular, put a stop to it. The Doctor and Ace had two other encounters with the Helix as well. (COMIC: The Mark of Mandragora, Darkness Falling, Distractions)

21st century
Having sent out "sparks" to China and London to test the waters, Mandragora reappeared in London in May 2009, using the MorganTec computer systems company to spread its energy over the Internet. It decided that it was wrong about humans. Instead of stopping them, it would help them travel to the stars, acting as a leech all the while.The Tenth Doctor and Donna Noble, with help from Wilfred Mott, were able to throw it back into space, confused and with missing memory. (PROSE: Beautiful Chaos)

Behind the scenes
Secrets of the Stars was originally going to use the Mandragora Helix. However, it was decided that "Mandragora had to change too much, and was too easily defeated, in order to fit this plot" and the Ancient Lights were created instead. Russell T Davies has said he likes to think both entities are "distant cousins". (DWMSE 23)