Story arcs
Story arcs are story lines in Star Trek that are told over the course of multiple episodes. They are not simply two-parters or recurring characters and themes, but rather plots that are interwoven with other arcs and plot threads. An example of this is s introduction of the Dominion and the eventual Dominion War. 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.

Prior to DS9, story arcs were a relatively minor part of the Star Trek universe.  and  both largely restored the status quo ante at the end of each episode, and even two-part episodes were somewhat rare. This changed due to the stationary nature of space station Deep Space 9, which did not simply move on to the next adventure each week; characters' actions had lasting consequences, and the events of one episode directly influenced the next. At the time, Ira Steven Behr had to fight with  over making the show so serialized. 

 took the idea of the story arc in a different direction by setting itself aboard a starship as per the traditional Trek formula but stranding its crew in the distant Delta Quadrant. This both enhanced and reduced the prevalence of story arcs; while alien races such as the Kazon and Borg appeared in multiple episodes, the show was hampered by its very nature: the object was to leave familiar elements behind, which meant each plot thread had a limited life span.

, like DS9 before it, often relied on story arcs such as the Temporal Cold War and the Xindi arc that took up the entire third season. By the show's fourth season, Enterprise wrapped up these story arcs and instead refocused on the show's prequel concept with a series of "mini arcs." Most season four episodes are two- or three-part story lines, with few stand-alone episodes.

Feature-length episodes
These episodes are originally broadcast in two hours, as opposed to the standard one hour. After their original run, feature length episodes are re-cut as two part episodes (see below), but are usually released in their original broadcast format as a single episode. They include:

Two-part episodes
These episodes air separately, but tell the same story. It is typical for the first part to end with the line "To Be Continued...". They are frequently used to end and begin seasons. Two-part episodes include:
 
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Three-part episodes
Three consecutive episodes that air separately, but tell the same story.
 
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Multi-episode arcs
Multi-episode arcs tell a continuing story and are spread out through several different episodes throughout one or multiple seasons.

The Next Generation
 Q and the Enterprise
 
 
 
 
 
 
 
 
 Worf vs. Duras
 
 
 
 
 
 
 
 
 
 Sela

Deep Space Nine
Changeling infiltration

Klingon War

 Eddington vs. Sisko
 
 
 
 Dominion Invasion
 
 
 
 
 
 
 
 
 The Final Chapter

Voyager
 Voyager vs. the Kazon
 
 
 
 
 
 
 
 
 
 Q Civil War
 
 
 
 The Hirogen's Hunt
 
 
 
 
 
 
 Barclay and the Pathfinder Project

Enterprise
Temporal Cold War

 
 
 
 
 
 
 
 
 

 vs. Andoria
 
 
 
 
 
 
 
 Journey to Risa
 
 
 
Archer's trial by the Klingons
 
 
 
 Xindi War

Discovery 
 
 
 
 
 
 
 
 
 
 
 
 
 The Red Angel
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 The Burn
 
 
 
 
 
 
 
 
 
 
 
 
 
 The DMA

Picard 
 Synth mystery

Lower Decks 

 Pakled conflict

Films 

 Spock's death and resurrection, and the consequences thereof

Subject arcs

Section 31 
22nd century episodes
 
 
 
 
 

23rd century episodes

24th century episodes

The mirror universe

The alternate reality

Q 
Q-related episodes

Non-consecutive arcs
Starting in...

The Original Series 
The Talosians
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 Polywater intoxication
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 Shore Leave Planet
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 Kor
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 Khan Noonien Singh
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The Next Generation 
 DaiMon Bok and his revenge attempts on Picard
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 The Traveler and his interactions with Wesley Crusher
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 Lore
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 The Crystalline Entity
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 Alien neural parasites infiltrate Starfleet Command
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 Professor 
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 Arridor and 
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 Vash and her relationship with Jean-Luc Picard and Q
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 Thomas Riker
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 Riker and the Pegasus
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 Borg and First Contact (the Borg's involvement with Earth's first contact in 2063 and the repercussions which followed)
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 Vulcan/Romulan Reunification
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Deep Space Nine 
 Anti-alien sentiments on Bajor
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 Bajor's entry into the Federation
 DS9 Season 1, 2, 3 and through 4, 
 The Maquis' struggle for self-determination
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 The Dominion's threat to the Alpha and Beta Quadrants
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 Kira and Odo
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 Kira and Dukat
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 Quark and Grilka
 
 O'Brien and Liam Bilby
 
 Dominion cold war
 , DS9 Season 4 (esp. , , and ), , and 
 Nog and AR-558
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Voyager 
 The Hirogen and holographic technology
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 The Silver Blood
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 The Q Continuum
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 Fair Haven
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Enterprise 
 Augments and Khan Noonien Singh
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 Xenophobic Humans
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Discovery 
 Harry Mudd
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Short Treks 
 Rise of the Kelpiens
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 Tribble troubles
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Picard 
 The Conclave of Eight attacks Mars (prologue flashbacks in chronological order)
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Films 

 The destruction of Romulus
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Plot devices