As has been noted, the series has been getting goofier, though chronologically. NETRICSA was installed hastily to give Serious Sam an edge when fighting Mental's forces, both in the current age and in the past. But, be it an unexpected virus, untested technology
, or just having a powerful computer implanted in the brain,
NETRISCA is damaging Sam's brain, and causing strange visions and hallucinations.
BFE has barely any strange visions, though a few start to pop up around TFE, notably the giant-headed Croteam members and the pyramid of crates. A few more oddities occur in TSE, notably the Croteam ship that takes out the space ship.
By Serious Sam 2, NETRISCA is heavily corrupted and causing massive damage, including Sam now able to hear NETRISCA, the fairy-tale planets, the game show, and the craziness with searching out the amulets, only to hallucinate seeing a pile of them at the end.