The Laptop Intersect refers to a portable version of the Intersect 2.0 which is supposedly an Intersect made entirely by Stephen Bartowski (Orion), without any government modifications. It is presumed that the CIA/NSA 2.0 files inside Chuck's head were overwritten by the laptop Intersect.
In the Season Four episode "Chuck Versus the First Fight", Chuck's mother surprises Chuck inside Stephen Bartowski's secret base and uses a Portable device on him which suppresses the Intersect 2.0 inside Chuck's head rendering it inoperable and putting Chuck in danger. Whilst Team Bartowski and the CIA/NSA scientists attempt to get the Intersect working, Ellie and Devon are mainly responsible for Chuck getting the Intersect back.
When she and Devon attempt to switch the Laptop they find out that it's broken, Devon calls in Nerd Herders Jeff and Lester who agree to fix the Laptop in exchange for free medical examinations for most of the Buy More staff. Once the Laptop is fixed, Devon and Ellie switch it on and discover that a password is needed, with the password hint being "Knock, Knock". Ellie guesses that the password is "I'm here", a reference to her childhood habit to mix up jokes. As soon as she types it in, the computer comes to life and Ellie is stunned by whatever is displayed.
Stephen's laptop presents Ellie a memory problem which she solves by doing MRIs on herself. She saw that Stephen was trying to store information in the brain but was going about it the way of an engineer, and not how the brain actually stores information. She uploads this information into the computer and it prompts for another password "1 or 11".
She doesn't know the answer to this question. Later after they have had dinner with Mary and Volkoff, Devon gives the laptop to Chuck. Realizing the question is a reference to blackjack, Chuck inputs as a password "Aces, Charles" and the laptop activates again, and flashes (essentially repeats the original process from Bryce Larkin's email) Chuck with a version of the Intersect. Chuck falls on his back, but flashes on kung fu to jump back up.
NCS Possession Edit
In "Chuck Versus the A-Team", the laptop is revealed to have been in CIA possession. However, it was modified by CIA division NCS to remove human emotions from it's users, which is believed to make Intersect agents perfect. The project was disbanded by General Beckman when two new human Intersects have failed to disarm a nuclear bomb, whereas Chuck managed to do it himself.
The NCS Intersect was removed from the NCS agents, and the two are dismissed. NCS Deputy Director Jane Bentley did not tread lightly on the dismantling of her operation, and sent the laptop to Ellie as a Bartowski is far more capable of handling an Intersect.
Ellie's research Edit
Whilst the Laptop was in Ellie's possession she begin looking into her fathers research that was stored on the laptop. She identified the research as her father trying to store information in the brain but was going about it the way of an engineer. Jane Bentley is seen monitoring Ellie's activity on the laptop.
After discovering files on Agent X, Ellie tells her mother, Mary about it.
After this she is shown working for long periods of time every day on her father's research, presumably working at the research from a doctor's point of view. It could be concluded that the research Ellie did in what basically is the Intersect could have significantly changed how the Laptop Intersect's version of the Intersect 2.0 model works.
One change that she could have made, that we have been seeing, is that the Intersect is more easily uploaded as seen from Victoria, Richard and Morgan being able to upload it. It is also theorized that Ellie's changes may have fixed some of negative Effects that the Intersect causes, meaning that Human Intersects may no longer need to use the Governor.