As seen in The Deadly Assassin, the Eye was linked to two other Gallifreyan artefacts, the Sash of Rassilon and the Great Key of Rassilon. The Sash was needed to control the Eye safely without being sucked into it, and the Great Key was an ebonite rod that could be used to drain energy from the Eye. The Great Key was later renamed the Rod of Rassilon in The Invasion of Time (1978) to distinguish it from the other Great Key, a component of the De-mat gun.
In The Deadly Assassin and the 1996 Doctor Who television movie, the Master tried to use the Eye to give himself a new set of regenerations.
The first connection between Omega and Rassilon was made by Alan Moore in his 1980 Doctor Who Monthly comic strip story Star Death (DWM #47). Although the canonicity of the non-televised media is open to interpretation, Star Death showed the proto-Time Lords trying to collapse the star Qqaba into a black hole and harness its "energy stream". Omega and Rassilon were both members of this project, and when sabotage sent Omega hurtling into the newly created black hole, he was presumed lost. Rassilon then took control of the project, and the power of the black hole. It was not made explicit, however, that this black hole was the same one that provided the Eye of Harmony. (Qqaba would also be mentioned in the 1998 novel The Infinity Doctors by Lance Parkin.)
This connection appeared next in the 1988 serial Remembrance of the Daleks, where Omega's stellar manipulation device was dubbed the Hand of Omega and became the object of a struggle between two competing factions of Daleks. Although the televised story made no mention of Rassilon, the 1991 novelisation of the serial (though again of unclear canonicity) by the story's writer Ben Aaronovitch, drawing on elements of the so-called "Cartmel Masterplan", made the connection between the two Time Lords explicit. The story of Omega's supernova becoming the black hole that provided Rassilon with the Eye of Harmony became part of the fan-accepted mythology and was incorporated into the Virgin New Adventures novels.
However, having the Eye of Harmony on board the TARDIS contradicted the idea that the Eye itself was on Gallifrey. To reconcile this, fan speculation held that this was not the real Eye, but merely a name applied to a remote link to the actual Eye that powered the craft (possibly in the same way the Time Lords transmitted energy from Gallifrey to the TARDIS in The Three Doctors), or alternately, the Eye had been somehow transferred to the TARDIS. The former conjecture became established fanon, and was taken up in the spin-off media and was eventually confirmed by the official BBC website.
The Past Doctor Adventures novel The Quantum Archangel by Craig Hinton offered another explanation by claiming that all TARDISes built after a certain point, including the Type 40 the Doctor uses, have a mathematically modelled duplicate of the Eye with all its attendant features.
In the episodes "Boom Town" and "Utopia", the TARDIS needed to "refuel" by absorbing energy from a "scar" left by a closed spacetime rift, implying that it is not powered entirely by the Eye at this time. The former episode also revealed that the TARDIS console concealed the "Heart of the TARDIS", a mysterious glowing energy source that the Doctor associated (in "The Parting of the Ways") with the energies of the time vortex.
The Tenth Doctor makes an oblique reference to the Eye's creation in the episode "The Satan Pit" when he quotes: "My people practically invented black holes. Well... in fact they did."