Prior to DS9, story arcs were a relatively minor part of the Star Trek universe. Story arcs often take precedence over other plot elements and consume a series for several consecutive episodes, but in many cases (such as the Dominion War) they may take a back seat and re-enter the picture later on. An example of this is Star Trek: Deep Space Nine's introduction of the Dominion and the eventual Dominion War. They are not simply two-parters or recurring characters and themes, but rather plots that are interwoven with other arcs and plot threads.
Story arcs are story lines in Star Trek that are told over the course of multiple episodes.