The ORACLE

The Oracle summoned Optimus Primal and reformatted him and his Maximals into their techno-organic forms. It is with his communion with the Oracle, that Optimus Primal is able to see visions. The Oracle is able to appear and disappear at will. Within the Oracle lies...

VECTOR SIGMA

Vector Sigma first appeared in the Transformers episode "The Key to Vector Sigma." It was revealed in that Vector Sigma was a supercomputer buried deep within Cybertron's core. Vector Sigma also had the ability to bestow life to Transformers, when activated by the Key to Vector Sigma, which was guarded by the ancient Autobot, Alpha Trion (who became one with Vector Sigma when he died). Vector Sigma gave life to the Stunticons and Aerialbots.

Some time after the Great War, Vector Sigma declared itself as the omnipotent god of all Transformers (as seen in Beast Wars Neo). Not only that, but Vector Sigma had also established itself as the supreme consciousness of planet Cybertron (Sabretron). This attracted Unicron's attention who came to Cybertron and possessed Vector Sigma, making Cybertron his new body. Unicron was ulimately stopped by Lio Convoy and Big Convoy. 

Some time after that, Vector Sigma merged with the Matrix and became the Oracle (perhaps to prevent Unicron from possessing it again). It's possible that the Oracle's sentience is actually Vector Sigma. There are two reasons for this -- first of all, Vector Sigma has always been sentient (Vector Sigma once told Optimus Prime, "before Cybertron was, I was"). Secondly, Vector Sigma is able to commune directly with other Transformers. In Beast Wars Neo, Vector Sigma often communed with Big Convoy. We see the Oracle doing the same thing in Beast Machines.

The MATRIX

Above: Rhinox has become one with the Matrix.
The Matrix was first seen in the Marvel comics. Decepticon leader Shockwave beheaded Optimus Prime in order to use the Matrix to give life to some Decepticons.  The Matrix was seen in a physical form in "Transformers The Movie," where it was revealed that it was the only thing that could destroy Unicron. The comics later revealed that the Matrix contained a portion of Primus' life essence. 

In Beast Wars, the Matrix was referred to as a realm where deceased Transformer Sparks rested. This follows on from Optimus Prime's line in Transformers The Movie, "soon I shall be one with the Matrix." In Beast Machines, the Matrix is clearly shown as a countless collection of Sparks, manifest within the Oracle. 

 
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