The roots of the Karotechia are deep and varied. When the unit was officially created within the Ahnenerbe in 1939, it drew its members from within the Ahnenerbe, the disbanded Thulegesellschaft, and a little known section of Archive Department VII of the Reichssicherheitshauptamt (RSHA, Reich Security Central Office) called Sonderkommando-H. Created in 1935 under direct orders from Heinrich Himmler, Sonderkommando-H (for Hexen, German for witches) collected records of the Catholic Inquisition against witchcraft from libraries in Germany and Austria. These records were collated into the Hexenkartothek, a catalog of over 33,000 index cards, each providing the details of a victim of the witch trials. While most of the Hexenkartothek concentrated on witch trials in Germany, Sonderkommando-H researched cases from as far away as India and Mexico.

The research of Sonderkommando-H was meant to provide propaganda that would justify an SS crackdown on the Catholic Church, as well as discover the ancient Germanic religion that Himmler believed had been eradicated by the Inquisition. The SS officers that collected the Hexenkartothek came to informally refer to themselves as the "Kartothekia," and what they discovered were arcane formulae and necromantic rituals. Enough was learned by Sonderkommando-H to create what some one hundred and fifty known witches, warlocks, and alchemists termed "the resuscitating of ye vital saylts." This formulae was first successfully put to effect by SS-Hauptscharführer Dieter Scheel when his team resurrected 17th century sorceror Jurgen Tess. It was this incident that created a new department within the Ahnenerbe to exploit the occult in service to the Reich: the Karotechia.

Occult research had been conducted by various arms of the SS for quite some time before the creation of the Karotechia. In the Ahnenerbe, the Abteilung zur Überprüfung der Sogenannten Geheimwissenschaften (literally, Department for the Examination of So-Called Secret Sciences) had analyzed the occult since 1933. Also since 1933, Karl Maria Wiligut and his Department for Pre- and Early History had been Himmler's premier occultist, a position that was undermined soon after the creation of the Karotechia. Suitable members of these organizations were drawn to the Karotechia, as were former members of the Thulegesellschaft and scholars from Nazi-allied regimes and occupied countries. Kabbalists and Gypsy practitioners were even forcibly recruited out of concentration camps, as well as those occultists rounded up through Aktion Hess.

Moreso than any other group researching the paranormal for their government during the Second World War, the Karotechia sought to exploit the occult to its fullest. With the full backing of the SS and the Nazi state, they raided the libraries and museums of Europe in an insatiable search for arcane power. No avenue of study was left unexplored, no matter how ridiculous it might seem to the more established academics of the Ahnenerbe. The Karotechia was shielded from inquiry within and without by direct patronage of Himmler, who passed certain information on to Hitler (the Führer remained basically unaware of the Karotechia). Members of the Karotechia were known by their initials in SS documents, and by their rune-names in internal correspondence, the names given upon induction into the unit. They were identified by the sonnenrad runes worn on the lapels of their black Allgemeine-SS uniforms. This insignia and the men that wore it were equally feared and respected throughout the SS.

The Karotechia never had a central headquarters, as each project maintained its own base of operations, reporting directly to Himmler. When the Karotechia was required to perform some ancient Germanic ritual for Himmler (virtually always ineffectual), they were called to the SS-order castle at Wewelsburg. However, the isolation and provincial boredom of the place meant that the Karotechia officers preferred to conduct their operations elsewhere. This also allowed them to operate with great independence.

Never as successful as their reputation belied, the Karotechia did score a number impressive victories during the war. In particular was the discovery of a Gothic version of the Necronomicon in the spring of 1944, which opened up several new projects to exploit its potential. Most of these projects ended in failure, causing great destruction, such as the incident at Castle Naudabaum in early 1945, where seven Karotechia officers and seventy-three support personnel were killed and the castle destroyed during an abortive attempt to summon an extraterrestrial being called Azathoth.

This disaster lead to the final Karotechia operation of the war: Aktion Gotterdammerung, the attempt by the Karotechia to reenact the Naudabaum disaster without aborting the sequence to summon Azathoth. Aktion Gotterdammerung was foiled by the American Delta Green organization. In the end, of the one hundred and sixty-four members of the Karotechia, fifty-four were assassinated by the Allies, six died of natural causes, three died during Allied bombing, four were executed for disloyalty, fifteen were killed while conducting experiments, nine committed suicide, eleven were institutionalized, twenty-four vanished while on operations, and thirty-seven escaped the destruction of Nazi Germany through the ODESSA network.