Intersect Glasses are glasses that contain (or can access) a portion of if not complete files for the Intersect.
Intersect update Edit
In the Season Two episode "Chuck Versus the Break-Up", the Intersect glasses were first seen and used to send an update for the Intersect in Chuck's head. The glasses were left inside Chuck's bedroom, courtesy of Bryce Larkin when he told Chuck that the latter would always make the right decisions.
It is unknown who ordered Bryce to update Chuck with these glasses as there is no mention of Sarah, Casey or Beckman knowing about the update. It could be said that Bryce had been working along side Orion for a while as they seem to have a relationship in "Chuck Versus the Ring". Further evidence that these glasses may not have been government issue is that, unlike all other Intersect Glasses featured in the show, these glasses needed the subject to be Identified before being uploaded.
In the Season Three episode "Chuck Versus the Nacho Sampler", revealed that the Ring was attempting to reverse-engineer the Intersect from damaged components of Intersect 2.0 they stole from the CIA after its destruction by Chuck.
As part of this effort, they contracted a software engineer named Manoosh Depark to develop a new Intersect. The results of the project were a pair of sunglasses that could "flash" an agent with Intersect 2.0 skills. Unlike the full Intersect, the portable version did not download into an agent's brain and was entirely self-contained within the device, however the extent of its capabilities are unknown, as the only flashes they have been seen to produce are on martial arts. The images during flashes were also grainier and not as clean as Chuck's. Manoosh ultimately destroyed his glasses when cornered, hoping that without a functional prototype, the Ring agents he was attempting to cheat would consider him too valuable to kill.
Corrupt Intersect Edit
The glasses appeared once more in the Season Four finale. Two weeks after Team Bartowski had been disbanded when Chuck went rogue to save Sarah, Clyde Decker intentionally left behind a pair of sunglasses containing a copy of the Intersect 2.0, but with Morgan being himself when it came to snooping around, put on the glasses and accidentally downloaded the Intersect into his brain.
This made him the new and only human Intersect on the now freelance Team Bartowski, after Chuck's Intersect had been suppressed. This new Intersect contained as Chuck speculated a Trojan Horse, which caused memory loss for Star Wars and Indiana Jones References. The Trojan Horse altered Morgan's personality, making him more overconfident and arrogant, so much so that he dumped Alex via text.
Second Corrupt Intersect Edit
In Chuck Versus Bo, it is revealed that while corrupted by the Intersect, Morgan came across another pair of Intersect Glasses in Vail containing a copy of the Intersect 2.0 acquired by Nicholas Quinn who orchastrated Morgan's capture in order to verify the claims of the Intersect having side effects (as Morgan's did). Upon deeming Morgan healthy he decided to knock him out as there would be nothing for him to worry about. As he sprayed the X-13 knockout gas, Morgan 'zoomed', breaking out of his restraints, knocking out everyone in the room including Bo Derek before escaping with the glasses and hiding them in a videogame display vault in the Vail Buy More.
Once the glasses are in the custody of freelance Team Bartowski, Chuck is captured by Quinn, who orders Sarah to bring the glasses to the San Pedro pier. Once Sarah and Casey arrive they realise it was a setup and are surrounded with Quinn's men demanding she hand over the glasses without giving her Chuck. Casey opens fire, allowing Sarah to hide but they both soon realise they are running out of ammunition and are heavily outnumbered. Seeing it as the only option, Sarah puts on the glasses and uploads the Intersect, taking out all the men.
However in Chuck Versus the Bullet Train it is shown that it is the exact same copy as Morgan's, containing a Trojan Horse as she begins to suffer from its effects. When fighting Quinn she was unable to stop flashing when she tried, resulting in her kicking him out the train window. It was thought that it would take a much longer time for any damage to be done however it is discovered by Ellie after examining Morgan in Castle that the effects take place the more the host flashes. Morgan started losing his memory within a month of his upload because he gradually began using the Intersect more as he went on missions while in contrast, Sarah had flashed 40 times in the space of just two days. To prevent any further damage being done Sarah was blindfolded in order to avoid any stimulation that might cause her to flash, but was already showing signs of being compromised by the program, such as not remembering who Alex was. Upon being captured later by Quinn he used cards with special designs to stimulate flashes until she lost her memory, waking up in her apartment with him telling her that he was her CIA handler and that her next mission was to kill Chuck. Quinn has removed the Intersect from Sarah with a Suppression Device.
Final Pure Intersect Edit
The Final version of the Intersect left in the entire world was housed at DARPA. Chuck was subtely coerced into breaking in to it (courtesy of a brain-washed Sarah who was working for Quinn) to destroy it. Instead Sarah downloaded it and attempted to deliver it to Quinn, but was thwarted by Chuck, who snatched the glasses as he realized that the Sarah with him didn't have her real memories. This Intersect was also corrupt. However, Quinn had located a Key, developed by Stephen Bartowski that permitted re-programming and fixing corrupt Intersects.
He sought the three pieces of the key (broken down by Stephen for security purposes and handed to two other people including Hartley Winterbottom who later became Volkoff). Chuck planned on using this Key to try and restore Sarah's memories (by uploading her Mission Logs along with memory triggering images such as those from their Wedding Album into the Intersect). However, he was forced to use the fixed Intersect on himself using the glasses in order to defuse a bomb set in the Pacific Concert Hall by Quinn in his failed attempt (courtesy of Team Bartowski) to obtain the 3rd part of the key from Beckman (who had been given Stephen's part of the Key). Since there is no mention of Chuck asking to have the Intersect removed and since he has fully working Governors, it can be assumed he decided to keep this final, working version of the Intersect.