That's a lot of questions.

• The matrix is a virtual reality. The dark tunnels, the breeding grounds, the Nebukadnezar, the bad food, etc... is the real reality,
• Thomas Anderson is a real person only in the perspective of everybody in the virtual matrix,
• The red pill did not transform Thomas Anderson, it kind of killed him: The red pill was a "virus" that the matrix program could not handle, thus so releasing Neo from its incubator, and "sending" a tracking signal to the code stream of the matrix which is intercepted by Morpheus' team. Neo woke up, became aware of the reality for the first time in his life and Thomas' code was purged from the matrix,
• Morpheus tells Thomas that when he takes the red pill, he simply will tumble into a rabbit hole giving nothing but the truth. The red pill does not plug him into the matrix, nor did Morpheus say so,
• Thomas was pursued by the agents from the moment the matrix program recognized the goal/plan of Morpheus' team. The very beginning of the movie reveals Trinity searching for Thomas. Of course the agents went after Trinity first,
• The oracle tells Neo a lie because the one had to find things out for himself. Also, he kind of becomes the one by almost sacrificing himself due to the lie, but that's a whole different discussion with surely lots of opinions.

That's a lot of questions.

• The matrix is a virtual reality. The dark tunnels, the breeding grounds, the Nebuchadnezzar, the bad food, etc., is the real reality.

• Thomas Anderson is a real person only in the perspective of everybody in the virtual matrix.

• The red pill did not transform Thomas Anderson, it kind of killed him: The red pill was a "virus" that the matrix program could not handle, thus so releasing Neo from its incubator, and "sending" a tracking signal to the code stream of the matrix which is intercepted by Morpheus' team. Neo woke up, became aware of the reality for the first time in his life and Thomas' code was purged from the matrix.

• Morpheus tells Thomas that when he takes the red pill, he simply will tumble into a rabbit hole giving nothing but the truth. The red pill does not plug him into the matrix, nor did Morpheus say so.

• Thomas was pursued by the agents from the moment the matrix program recognized the goal/plan of Morpheus' team. The very beginning of the movie reveals Trinity searching for Thomas. Of course the agents went after Trinity first.

• The oracle tells Neo a lie because the one had to find things out for himself. Also, he kind of becomes the one by almost sacrificing himself due to the lie, but that's a whole different discussion with surely lots of opinions.