The KND Splinter Cell is supposedly a traitorous shadow group within the Kids Next Door Organization who intend to destroy all adults on Earth, good or bad. A group that is unknown to Supreme Leader Numbuh 362 or most KND operatives. The actual Kids Next Door are only against evil adults, not adults in general.
The KND Splinter Cell was possibly created after the incident in Operation: Z.E.R.O., when Father recommissioned Grandfather to destroy the KND, using "Numbuh Zero's Recommissioning Device" (used in Operation: E.N.D.)
The Splinter Cell was first mentioned in Operation: M.E.S.S.A.G.E., in a note reading "The Splinter Cell is real."
Throughout Season 6, the Splinter Cell is seen monitoring and manipulating Numbuh 1, intending to ensure that his emotional links were severed and his loyalty to the KND unquestioning, starting in Operation: W.H.I.T.E.H.O.U.S.E.. In Operation: G.I.R.L.F.R.I.E.N.D., their actions cause Nigel's long-time girlfriend Lizzie to leave him.
In Operation: I.N.T.E.R.V.I.E.W.S., the Splinter Cell is revealed to be a cover for the Galactic KND. The purpose of using the Splinter Cell to cover up the GKND's tracks is for the good of the KND as a whole, because according to Numbuh 74.239, the organization isn't ready to know about the GKND just yet. The entire time, they were testing Numbuh 1 to determine if he was fit to join them as Earth's representative among the GKND. Number Infinity, Numbuh 71.562, Numbuh 74.239 and Numbuh 274 are known to be associated with the Splinter Cell. The series then ended abruptly after the episode Operation: I.N.T.E.R.V.I.E.W.S..
Not much else is known about the splinter cell or the GKND, but it is presumed that they may have ulterior motives, according to the leaked teaser for Galactic: Kids Next Door.