Innocuously Important Episode

An episode that subtly sets events in motion that lead to a big payoff later on in the Story Arc. After The Reveal, the episode will suddenly take on much greater significance in retrospect.

May use a Chekhov's Gun and related tools, but telegraphing is avoided. Compare with Arc Welding where a Story Arc is created retrospectively from isolated episodes.

The examples, naturally, contain major spoilers.

Anime and Manga

 * Soukou no Strain: The Fan Service episode redeems itself by setting up a major plot point that, later on, leads to many a Heroic BSOD, the outing of Sara's identity, the cementing of the True Companions, and the death of one unexpected major character.
 * Madlax pulled this off with its Beach Episode, of all things.
 * Fullmetal Alchemist loves doing this. The only even slightly minor character who has only one appearance was the terrorist from the fourth chapter. Even he shows up again. Both Bald (and Colonel Genz from the video game) appear in an advertisement for automail in chapter seventeen.
 * In the 2003 anime version, you didn't think Russell and Fletcher would be content helping Bellsio with his farm for the rest of the show, did you? It seems Russell enjoys borrowing Ed's identity a bit too much.  Also there's Rose.
 * Tengen Toppa Gurren Lagann: Episode Five seemed like a fairly basic Released to Elsewhere plot made in order to add to the adventuring party, but the themes in that episode proceed to permeate the entire third quarter with glorious darkness.
 * Gungrave: The first episode of the anime might seem like just another mindless shoot-'em-up, but in the second episode you suddenly get to the real story, which is a mob drama.
 * Cowboy Bebop has the episode Sympathy for the Devil. The first time through the episode might seem to be just another episodic romp, . However, the episode not only hints at , but it also has a lot of parallels with the finale, from.
 * The heartbreaking episode Affection in Stand Alone Complex is seemingly an episode made to highlight some of The Major's tragic backstory. Turns out it also . This does not become explicitly apparent until the final episode of the series.
 * Steins Gate: The first episode introduces the characters and setting, and begins to get into the concepts of time-travel used throughout the series, but

Literature

 * Harry Potter is slow paced but sets up Harry Potter. It set up  Even the romantic plot of Chamber of Secrets is revisited in Half-Blood Prince, but with the roles of  reversed.
 * Bridge of Birds: Every seeming Wacky Wayside Tribe turns out to be this by the end.
 * Dirk Gently's "holistic" philosophy isn't wrong in the context of the books -- even the aside jokes are relevant later on.
 * Grave Peril, the third book in The Dresden Files series, has serious implications reaching all the way out until Changes. (And likely beyond, as books continue to be released. Word of God says that all the guests at that little party will be seen again.)
 * The prologue to A Game of Thrones is like this to the entire A Song of Ice and Fire series. The prologue to A Feast for Crows serves the same function within that book, setting up plot that doesn't truly get put into motion until the last chapter, some 900 pages later.

Live Action TV

 * Babylon 5. Several episodes of the first season.
 * The thirteenth episode "Signs and Portents". The episode's "A" plot is some fairly standard and unimportant thing involving Raiders [space pirates] and a Centauri artifact called The Eye. The "B" plot, involving the first appearance of the enigmatic Mr Morden and the question "What do you want?", turns out to be incredibly important and crucial to the rest of the series -- but the episode's retrospective importance only kicks in at the first season finale.

Its importance was lampshaded by the fact that the entire first season was also named "Signs and Portents" (though a casual viewer wouldn't know this - the season titles only appeared on fan sites.) "Portents", of course, are hints about future events.
 * The A Plot does have one rather important thing happen in it; it's the first appearance of The Shadows.
 * "MidnightOnTheFiringLine" (the first episode after the pilot movie) featured subplots and character moments that the show kept referring to throughout many of its best moments over the rest of its run. In fact, it is this trope's former Trope Namer.
 * "Infection", the fourth episode of the show, managed to introduce several elements that would become very important later on, including Interplanetary Expeditions, ISN, Earth's desire for advanced biotechnology and the first mention of previous Shadow War a thousand years ago - and certain revelations about Sinclair's past and how it drives his behaviour in the present. Not bad for what is almost universally considered to be a lackluster Monster of the Week episode.
 * Doctor Who
 * The ending of "The Shakespeare Code" included William Shakespeare using words to stop the villains. The last episode in the season, "Last of the Time Lords", took that concept and turned it Up to Eleven.
 * "The Long Game" sets up a lot of later events- including the Ninth Doctor's regeneration- as the Doctor's actions lead to "Bad Wolf". Meaning of course that it also has perhaps the most relevant title of the entire show.
 * "The Unquiet Dead", which introduces the Rift in Cardiff. Without that rift, the events in "Boom Town", the show's first, third and fourth series' finales and The End of Time would not have taken place... nor any of Torchwood.
 * Classic Who also had Silver Nemesis (Cybermen vs Neo-Nazis) but it set up the Wolves of Fenric arc with Ace and the Doctor as Chessmaster motif which concluded in rather sinister style in The Curse of Fenric.
 * "The Lodger" seems like a filler episode (albeit a fun one), but we later learn that.
 * In series 3 of New Who, the episode "The Lazarus Experiment" set up both, and.
 * Similarly, "Human Nature" and "The Family Of Blood" appeared to be an updated telling of a Doctor Who novel, leading to a unique circumstance where fans familiar with the spinoff media were actually less likely to realize these episodes were this trope, which comes off as exceptional filler otherwise.
 * Lost : The season 3 episode "Flashes Before Your Eyes" seemed odd at the time. However, this was the first episode to employ any kind of time travel, and laid the groundwork for everything that has happened in season 5 with Ms. Hawking.
 * How I Met Your Mother: At first glance the "Showdown" episode seems like pure filler with Marshall and Lily preparing for their wedding and Barney going on The Price is Right. However, we learn two episodes later that
 * In Star Trek Deep Space Nine, a random Ferengi comedy episode "Rules of Acquisition" reveals that something called "the Dominion" is a major power in the Gamma Quadrant. The war against the Dominion is the Myth Arc of the show.
 * Stargate Atlantis: In the first season, they encounter a planet that had been developing a drug that would make them immune to the Wraith feeding on them, but also has a 50% chance of killing the person injected. It seems like a one-off story, until the middle of season 4 when their enemy, a Wraith-turned-human-turned-hybrid gets hold of the drug and begins to spread it across the galaxy. It plays an important role in several episodes from then to the end of the series.
 * Farscape:
 * "Beware of Dog" had a fairly ridiculous main plot, with a B plot of Crichton going crazy and imagining Scorpius around every corner -- but it's a brilliant setup of the entire plotline for the rest of the season, one that would continue throughout much of the series.
 * The very first time Crichton hallucinated Scorpius was in "Crackers Don't Matter", a nutty, off-the-wall episode where everyone's going crazy and fighting over crackers.
 * "A Human Reaction", a well done though not especially memorable episode - until it's revealed a few episodes later that the major plot point of the entire series was set up during its events.
 * Buffy the Vampire Slayer.
 * Three major villains in Season Six were all introduced through previous, seemingly "filler", episodes.
 * "I Was Made To Love You" (and earlier, ) seemed a bit out of place at the time of airing (robots? really?) but set up the suspension of disbelief needed for the Buffy Bot to exist in that series, which allowed Dawn to stay in Sunnydale after the events of "The Gift".
 * 'Killed By Death'. Buffy is sick and ends up in hospital - a place she hates since her favourite cousin died in hospital when they were children. While the Monster of the Week in the episode (which was also responsible for her cousin's death) is dealt with, Sunnydale General ends up playing a big role in Season Five - not only does Buffy's mother Joyce end up with a brain tumour and spends a few episodes there, but we're also, at the same time, introduced to the character Ben Wilkinson, a young medical intern who serves as a possible Love Interest to Buffy.
 * The Pushing Daisies episode "Circus Circus". No other episode sets up as many of the major arcs and themes in the second season: the corrosive effect of secrets; something new beginning as necessarily implying something else ending; stasis as the opposite of life/death/rebirth; the impossibility of simply picking up a relationship where it was left off; one's persona or public self versus one's True Self; a parent's inability to recognize his or her child.
 * The Battlestar Galactica Reimagined first-season episode "Tigh Me Up, Tigh Me Down" was thought to be a comedy filler episode revolving around a series of misunderstandings between Ellen Tigh (who unexpectedly reappears in the fleet) and Commander Adama (who believes Ellen is a Cylon sleeper agent). The whole episode climaxes in an amusing scene where everyone humorously works out their differences, and the matter is resolved. Three seasons later, in "Sometimes A Great Notion", it turns out this episode set up the eventual arc and reveal that.
 * The Mad Men third season episode "My Old Kentucky Home." On its face, the Four Lines All Waiting story serves as a series of character vignettes bound by the "work disguised as fun" theme. However, this episode introduces us characters that become prominent in later episodes (Connie Hilton, Henry Francis); and story arcs that carry through the next couple of seasons (Peggy's introduction to the counterculture, Joan realizing that marrying her doctor is not going to give her the life she thought she wanted, Betty looking for a way out of her marriage, among others).
 * Merlin had two:
 * In the first series "The Gates of Avalon" was a fairly basic Monster of the Week story, in which Arthur is targeted by two murderous Sidhe, but it also introduces the fact that Morgana is a seer which marks out her entire Character Arc from then on.
 * The third series had "Queen of Hearts", which seemed a one-off Filler which once more returned to status quo by the end of the episode, but it also introduced the character of "Dragoon", Merlin's old-man disguise which he puts to even greater effect in series four.

Video Games

 * In Dragon Age II, the whole first act is this. It sets up many plot points and characters that become important several years later.
 * In the original Kingdom Hearts, the story of the Deep Jungle world has Sora reacting to a slideshow picture of a large castle with an odd familarity even though he'd never left the islands before, and Tarzan telling Sora, in response to the question of where he can find Riku and Kairi, "Friends here; *&&X%.", which turns out to mean that his friends are in his heart.
 * A lot of seemingly comical or nonsensical things in Hatoful Boyfriend take on greater importance in the Bad Boys Love route.
 * In the first Mass Effect game, there's a side mission that involves going to the Moon and helping shut down a rogue AI. The third game reveals that.

Webcomics

 * Gunnerkrigg Court seems to be using this heavily, as several chapters, characters and plot points that seemed to have nothing to do with the overall Myth Arc at the time (particularly ) have taken on greater importance later, especially after the events of Chapter 20. The second chapter seems to be the only true example of a Filler episode so far. The second chapter contained set-up for what is now confirmed to be an Aborted Arc.
 * Homestuck's intermission at first seems to be a completely unrelated, silly tangent that has no bearing whatsoever on the plot. Of course, everything in Homestuck is plot-relevant, and said intermission turned out to have a big impact on For some, as much as the first three acts could be considered this, appearing to be nothing more than a bunch of pointless gags, but in actuality setting up a lot for later on such as

Western Animation

 * Transformers: Beast Wars
 * An episode near the end of the first season entitled "Before the Storm," which sets up the first season finale and a huge chunk of the second and third season subplots as well.
 * Similarly, the second-last episode of the first season of Transformers Animated, "Nature Calls", was an odd episode that involved "space barnacles", but it also set up for.
 * Also in Animated, the episode "Headmaster" seemed to just be another disconnected episode with a new human supervillain, except that the Headmaster would up responsible for (one of) Starscream's current predicament(s), as well as the introduction of Dirt Boss and the resultant effect on the Constructicons.
 * Star Wars the Clone Wars has the fourth episode of the second season seem like padding but it became the first of the five-part arc about the second invasion of Geonosis with the most gigantic battle thus far and the introduction of  in the show.
 * The Camp Lazlo episode "The Engagement" contains ends with a joke where, after Jane's engagement falls apart, rather then recognize Lumpus' affection she starts flirting with the Navy Turtle, hoping to be engaged to him. The final season sees Lumpus attending their wedding and subtly crashing it, beginning his relationship with Jane.
 * The Ed, Edd n Eddy episode "Ed, Pass It On" (from 2002) is about Eddy lying that his elusive older brother is returning to the cul-de-sac in an attempt to gain respect. When he supposedly does arrive, Eddy reacts with absolute fear. Seven years later, the Grand Finale Movie reveals that
 * In the same episode, when Rolf gets the "news" that Eddy's Brother is coming, he barricades his farm and tells Eddy to tell his brother Rolf's chickens no longer exist. After watching The Movie, it makes you wonder