The Intersect 2.0 refers to the second generation of the Intersect machines, which are more advanced than the originals and seem, now the government are aware that a Human Intersect is possible, to be geared towards being used on agents to turn them into super-spies. The Intersect 2.0, when inside an agent's head grants the agent the ability for Physical flashes, the ability to upload knowledge into the agents head enabling them to perform complex fight moves without any training.
The governments Intersect 2.0 first features in the Season Two finale, "Chuck Versus the Ring". In this episode, after Bryce Larkin is killed by several agents of the Ring, Chuck makes the decision to download the new Intersect into his brain before using a device given to him by Bryce to cause a power surge in the computer which fries the Intersect cube, making Chuck the only human Intersect 2.0. The Intersect appears to be far more advanced than its predecessor in the terms of the console being hand print activated instead of requiring a password, the video consoles also show the images one after another without the pause or delay of static seen in the the original and prototype Intersects.
Whether due to their failure to capture the original Intersect or independently early in its original development, Fulcrum attempted to reconstruct their own Intersect. The earliest direct reference to this may be traced to "Chuck Versus the First Date", after the organization attempted to steal the Cipher.
In "Chuck Versus the Suburbs", after Sarah, Chuck and Casey successfully infiltrate a Fulcrum-fronted suburb, Sarah and Chuck hold a house-warming party. One of the neighbours informs Chuck that she finds him attractive, and attempts to entice him to visit her across the street sometime. When Casey finds out her husband has made bulk purchases of high power cabling which suggests he has been attempting to hack government information, Chuck is sent to visit her, pretending to be interested in sleeping with her. She seduces him, and handcuffs him to a bed. However, Chuck manages to get the keys and escapes into another room, where he finds a computer running what is presumably a test version of the Fulcrum Intersect. Chuck inadvertently starts the test, and falls unconscious when the information is uploaded into his brain. He escapes however, and it is revealed that both the neighbor and her husband are Fulcrum. When they realized Chuck had survived the test and was unharmed, they capture Sarah, Casey and Chuck, and force Chuck to upload the Fulcrum Intersect into his brain. He survives the upload, and eventually with Casey's help, uploads it into several Fulcrum agents brains, which appears to be either fatal or cause extreme injuries (some Fulcrum agents subjected to the Fulcrum Intersect are seen captured by CIA agents, however they are bleeding heavily.)
"Chuck Versus the Dream Job" reveals that the Fulcrum Intersect project is being headed up by Ted Roark. Stephen, a.k.a. "Orion" identifies this version of the Intersect as "Intersect 2.0", and calls it his baby. The device is significantly more advanced in appearance than the original Intersect and Beta Intersect, which used a traditional PC as its interface and required a cipher. The new Intersect however, only uses a cube. Roark has been unable to complete the project, but when Chuck breaks into the Roark Instruments building to try and remove the Intersect from his head, he comes across his father, who is attempting to get past several of Roark's guards. Chuck tranquilizes them, and the pair enter Roark's hidden Intersect room. Orion reprograms the Intersect 2.0 to try and remove the Intersect from Chuck's brain, but it doesn't work. Roark enters, and explains that there is a problem with Intersect 2.0, and captures Orion, who is subsequently forced to fix it for him.
In "Chuck Versus the Colonel" Stephen reveals that he secretly did what he originally intended to do before being captured: he successfully reconfigured the Intersect 2.0 Cube to erase the Intersect images from Chuck's head, and is apparently successful after getting Chuck to watch the images. Team Bartowski rescues Stephen and captures the Intersect 2.0 from Fulcrum.
In "Chuck Versus the Ring", when Stephen consoles with Bryce, he tells Bryce that he knows the new Intersect 2.0 has undergone extensive modifications from his original design. When he asks Bryce what the new Intersect is capable of, Bryce says, "You don't want to know". Bryce was slated to receive an upload from the new Intersect at the Intersect building, though he also brought along a device made to destroy the new Intersect along with the terminal and chamber. Bryce was mortally wounded in an ambush from several Ring operatives while entering the Intersect chamber and ordered Chuck to destroy it. Instead, Chuck downloaded the new system into his brain first, and then destroyed the Intersect 2.0 using the power surge device given to him. Downloading this new Intersect into his head made Chuck a Human Intersect again.
In addition to its intelligence data , one of the modifications to Intersect 2.0 "flashed" Chuck's memory with the knowledge of new skills; his first flash gave him the ability to do highly-advanced martial arts, allowing him to quickly dispatch several Ring agents surrounding him quickly. Josh Schwartz and Chris Fedak indicated that the changes Stephen added at the government's request were designed specifically for Bryce Larkin, who was cold and calculating and in total control of his emotions. Chuck's emotional nature now has a direct effect on the functionality of the Intersect and made it's behavior both unpredictable and potentially dangerous to those around him.
The Intersect 2.0 features prominently in Season Three and is still in use in Season Four, where Chuck uses it to flash not only on intelligence data, but also to briefly learn skills like playing the guitar, using a zipline, languages, dancing, and firearms training, as well as the more obvious martial arts. As previously stated, Chuck is often unable to "flash" using Intersect 2.0 if he is undergoing any form of emotional trauma, for example, his situation with Sarah throughout the third season.
As of the late half of the third season and throughout the fourth season, Chuck appears to have good control over his emotions as he is now able to flash in high pressure situations. This may be due to him being with Sarah and can openly discuss his spy life with Morgan.
Physical Flashes Edit
The Intersect 2.0, like the former Intersect, gives flashes of information but unlike former models it can supply the human Intersect with physical flashes. Physical flashes are when the Intersect supplies the host with information, via upload, on how to perform physical moves which ran the gamut from knowing kung fu, to a foreign language or how to play the guitar. He flashes on these skills just as they become useful for solving problems, which in "Chuck Versus the Ring" occurred just as Sarah was put in mortal danger. However Chuck is not always able to get theses physical flashes as the Intersect 2.0 was meant for "a real spy, like Bryce Larkin", who was cold, calculating and in total control of his emotions. Chuck's emotional nature has a direct effect on the functionality of the Intersect and makes him struggle to activate the Intersect when he wants to use it.
In early episodes of the third season, these skill flashes are shown to be able to directly control Chuck, or cause him to react automatically to the source of the flash. In "Chuck Versus the Pink Slip", he had to make a concerted effort to resist throttling Emmett, while in "Chuck Versus Operation Awesome" he launched into an angry tirade against a customer berating her in Thai and reflexively kicked Lester in the face.
The Laudanol pill Chuck took had suppressed all of his emotions in "Chuck Versus the Tic Tac", showing that Chuck's flashes are only a portion under the limits on potential physical flashes. The Intersect appears to have an accelerated and more intense flash, providing enhanced abilities and reflexes once the Intersect user is completely relieved of their emotions.
Sarah comments at one point that it looks like Chuck "Saw something really bright and tasted something really sour at the same time" when he flashes.
Known Abilities Edit
Negative Effects Edit
We find out in Season Three that long term use of an Intersect that's stored in a human brain can start having negative effects on that brain. It is possible that we saw this effect at the end of the second season when Orion flashed on the agents taking Bryce to have Intersect 2.0 uploaded, resulting in Orion suffering pain. What makes this even more likely is that Orion doesn't have a governor on at the time.
The negative effects the Intersect can have are bad flashes where the intersect images interfere with the users vision causing them pain. Chuck began to experience vivid nightmares that were eventually traced back to the Intersect itself, and Chuck's psychiatrist expressed concern that the Intersect may soon overwhelm Chuck's mind entirely. During the final two episodes of the third season, the condition has worsened while Chuck flashes on information or skills, causing him to suffer random flashes of information and a lingering ringing noise in his head. This prevents him from recovering from the flashes, leaving him vulnerable.
As of Season Four, Chuck begins using the governor at all times as it has become his life support. The research Ellie completed via the Laptop, looking at the Intersect from the POV of a doctor not an engineer may have lessened some of these problems.