Etymology

glitch in the Matrix

Today it means: An extremely bizarre event that seems to be only explainable by a glitch in the fabric of reality. Full definition →

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The story

Referencing the Matrix series of movies (1999–), in which humanity is imprisoned in a lifelike simulation of reality while machines have taken control of the "real" world. When the simulation in the movies malfunctions, unexplainable events happen. For example, in The Animatrix, there is a glitched house where gravity does not work consistently and rainfall is observed indoors.

Etymology from Wiktionary, CC BY-SA 4.0.