The First Intersect (also known as the original Intersect) was a computer system built for CIA Agent Nicholas Quinn prior to the first episode. Agent Bryce Larkin worked on the project until discovering that Fulcrum intended to steal it.
Bryce then steals the data and e-mails it to Chuck Bartowski. Beginning the events of the series, Chuck plays a game of Zork sent by the email and triggers the Intersect download, not knowing what it was, and becomes the Human Intersect.
It can be concluded that after long-term or excessive use of this Intersect can still cause a negative effect on the brain, but takes longer to take effect than the Intersect 2.0. These effects can be counteracted by a version of the Governor that Stephen Bartowski is commonly seen wearing.
A user who has subliminally retained the Intersect data receives feedback from it in the form of what have been labeled "flashes" by Operation Bartowski.
In each case, the flash itself is virtually instantaneous; however, the user experiences brief disorientation as he flashes. Chuck's handlers have learned to spot the subtle indicators (with spotty accuracy, so they frequently ask him if he has flashed), such as Chuck briefly going slightly cross-eyed and fluttering his eyelids, rapid wide-eyed blinking or suddenly exhaling and catching his breath. Another clue is Chuck suddenly showing fear as a result of passively flashing (see below) on something dangerous. Otherwise there is little external indication that such an event has occurred.
Stephen Bartowski has an early version of the Intersect in his head, which is apparently inferior to the finished product. His flashes apparently take longer than Chuck's, and the flash makes him momentarily go weak.
Early in the second season in "Chuck Versus the Break-Up", Bryce leaves Chuck a pair of sunglasses as a gift "for a real spy". When Chuck puts them on to see how they look in the mirror, a chip in the side activates, scans Chuck's eye for identification and starts uploading new encoded images, finishing the sequence with the words "Intersect Update Complete". The chip then self-destructs with a wisp of smoke.
Intentional Flashes (Computation)
In "Chuck Versus the Dream Job", Stephen Bartowski orders Chuck to use the Intersect in his head to perform a task, namely cracking a Feistel cipher to open a door in the Roark Instruments campus, which was shown to be beyond Sarah and Casey's technical ability earlier in the episode. Chuck protests that unless the data is already inside his head, he can't flash.
Stephen explains that as a designer of the Intersect, he knows its capabilities, and he tells Chuck to flash intentionally, which Chuck is able to do almost immediately with a little concentration. This is the first clue that the Intersect is more than a database, and can grant abilities as well