The Mandragora Helix originated in the Dark Times.
The Helix slipped inside the Doctor's TARDIS and traveled in it to late 15th century San Martino in Italy. Here it manipulated the local cult of Demnos, led by Hieronymous. It took over the cult's members, transforming them into energy beings able to kill with bolts of plasma.
It manifested again in 1863 China, where the Doctor confronted the Helix without fully understanding it, as the Helix encountered him in an earlier point in the Doctor's personal timeline.
As the the 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 Doctor and Ace, with the help of UNIT and Captain Muriel Frost, in particular put a stop to it. The Helix's appearance and modus operandi is remarkably similar to that of the Ancient Lights, which may have been a further manifestation of Mandragora.
In May 2009, the Helix reappeared in London, using the MorganTec computer systems company to spread its energy. The Doctor and Donna Noble, with help from Wilfred Mott, were able to stop it.
Some mysteries arose concerning the Mandragora. It did have a home but at the end of Beautiful Chaos it didn't know where it was. There was the fact that it possessed people, yet it is alluded to having a body of some kind, but this was unknown. It may simply existed as a Gestalt, like the Great Intelligence, or it may have a body that transition from mental to physical, like the Mara.
Behind the SencesEdit
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".