Orion's Intersect refers to the prototype Intersect which Orion (AKA Stephen Bartowski) is revealed to have downloaded into his head. This Intersect is only a prototype version of the First Intersect.
He reveals that when he was young and foolish he tested an Intersect prototype on himself. This, along with Stephen's Wrist Computer is possibly how he managed to stay on the run for so long when he had the CIA, NSA and Fulcrum pursuing him around the world.
Stephen Bartowski's Intersect is only ever seen in use once, but that one use easily shows that the earlier model is far surpassed by Chuck's. The intelligence is accurate, but its retrieval seems much slower, flashing one picture or document at a time with a noticeable gap between the images, rather than the cascade Chuck is usually subjected to.
It also visibly weakens or causes pain to Stephen, causing him to stagger and hold the wall to support himself once the flash has happened; whether this is due to a primitive Intersect, or the number of years Stephen been in possession of it, was not established.