Popular manga receiving extra story material is not a surprise at all. Spin-off manga is probably the most recognizable here in North America, mainly because we actually do receive them to varying extents (or there are fan translations out there), but another medium this comes from back in Japan is via the completely written word, i.e. novels. Whether they're light novels with plenty of images, sometimes drawn by the manga creator (lending it a good sense of canonicity), or more traditional novels, there are plenty of manga out there with extra material done in the style of prose rather than comic. Sometimes, even, these extra stories wind up getting adapted into their own anime incarnations. These adaptations can either be their own entire productions in their own right, or they might be inserted into the anime adaptation of the original manga as a type of "filler". To help showcase this occasional phenomenon, here are six examples of when anime studios went to novel spin-offs of popular manga.
Fullmetal Alchemist: The Land of Sand in Fullmetal Alchemist 
Hiromu Arakawa's Fullmetal Alchemist was, to put it extremely lightly, a big damn deal when it was adapted into its first TV anime back in 2003. The tale of two brothers, Edward & Alphonse Elric, who try their hardest to regain the humanity they lost in an alchemic revival of their mother gone wrong, the original manga story was only so far in when Studio BONES decided to turn it into an anime. For the most part, the first half of the anime stayed fairly true to the original manga story, and even elaborated on one or two scenes only vaguely mentioned in the manga, but two episodes in particular were not taken from the manga. Unlike some of the other filler featured in this anime's first half, however, these weren't exactly completely made up by the writing staff (lead by the infamous Sho Aikawa), but instead looked to a different FMA source. You see, by the time the 2003 anime debuted on Japanese TV that October, there were already light novel stories that were fully published, so the staff decided to adapt the first of them as a way to keep from catching up to the manga too fast.
The Land of Sand, written by Makoto Inoue, sees Ed & Al come to the town of Xenotime during their search for the Philosopher's Stone, as they heard a rumor of someone trying to use the stone to alchemise gold there in order to revive the dying city. Upon arrival, the two find out that another pair of brothers, Russell & Fletcher Tringham, are falsely using the Elric name in order to earn money to continue their reserach. Naturally, the older brothers (Ed & Russell) get into a fight over this, while younger two try to talk things out. If that plot sounds familiar, that's because you saw episodes 11 & 12 of the 2003 FMA anime, which was the very adaptation of this novel; in Japan the episodes used the novel title, while the English dub used The Other Brothers Elric. To be honest, after thinking about it, I will admit that those two episodes did seem to stick out very strongly compared to the other filler in the first half, and now it all makes sense why. In fact, Aikawa & his writers even brought the Tringham Brothers back for the end of the original anime, which had since gone into completely original material (which Arakawa encouraged the staff to do), though their involvement in the endgame was very minor; it was neat to see them one more time, however. It does make one wonder why the staff didn't just adapt the second novel, The Abducted Alchemist, as well, since it too had been finished up by the time the anime debuted. Of the ten novels that FMA had received, Viz did release five of them (all but the last two, plus none of the video game novelizations), but since The Land of Sand's story was so well known to the fanbase already, when Viz released a complete boxset for the entire manga in 2011, the extra space in the set was filled in with the fifth novel, The Ties That Bind, which was also penned by Inoue.
Fist of the North Star: The Cursed City as New Fist of the North Star
Notice the use of "as" instead of "in" just now? That's because this is the first of two entries in this list in which the novel adaptation was its own entire production, instead of simply being categorized as "filler". Tetsuo Hara & Buronson's Fist of the North Star is, I feel, a series that requires no introduction at all. After Ring ni Kakero set up the blueprint for modern shonen action manga, it was Fist that really took the genre out of sports & turned it into what we all know it as to this day. Though it really kind of overstayed its welcome due to the sheer popularity it had back in the day, the stuff after Raoh (& especially the post-Shura stuff that was never animated) is very rarely brought up nowadays, it's still overall one of the most important manga ever made. Considering that the head-exploding visual style of Hara was part of why it became so iconic, it's kind of odd to think that there was a novel made in the first place, but it does in fact exist. The Cursed City was written by Buronson, with the occasional piece of artwork done by Hara, & released back in 1996. Astonishingly enough, this story took place after the end of the manga, making this the last part of the post-apocalyptic Fist of the North Star timeline, & followed Kenshiro as he got involved in the battle between Freedom Village & Sanga, the dictator of Last Land, which has a cherished & uncontaminated water supply.
Considering that Toei Animation was such a big part of why the series became an icon by way of it's anime adaptations, both the two TV series as well as the infamously uber-violent movie, it's kind of surprising to see that Toei's last involvement with Fist was pretty minor. From 2003-2004 a three-episode OVA adaptation of the novel named New Fist of the North Star was co-produced by Toei, but the animation itself was done by A.C.G.T (Kino's Journey, GR -Giant Robo-), with direction by Takashi Watanabe (Boogiepop Phantom, Shakugan no Shana). At the very least, each episode was ~50 minutes long, & singing superstar Gackt not only performed the outstanding opening & ending themes, but was also the voice of Seiji, who acted as Kenshiro's martial arts rival for the story. Sure, Takehito Koyasu was oddly not quite fitting as Kenshiro (he'd be much better fitting as Rei for Tecmo Koei's Ken's Rage games), but overall New Fist isn't a bad production on the whole, and it's interesting to see a story that takes place after everything that Kenshiro had been through. It was brought over & dubbed by ADV Films back in the day, & it still gets kept in print, with the last re-release happening back in 2013.
D.Gray-man Reverse in D.Gray-man
With D.Gray-man Hallow currently airing as of the writing of this list, what better time to bring up Katsura Hoshino's Dark-Victorian story than now? When it first debuted in Shonen Jump back in 2004, D.Gray-man was definitely something different, & it rightfully became a notable hit, receiving its first anime adaptation only two years later. Said TV anime adaptation by TMS Entertainment wound up running for a good while, ending in late 2008 after 103 episodes. Naturally, with such a long anime series, that meant that filler was an inevitability, and there is a lot of it that is 100% made up just for the anime. Still, there are two pairs of episodes in the first half of the original anime that were taken from a novel spin-off. Said spin-off would be D.Gray-man Reverse, which was a trio of novels written by Kaya Kizaki (Dragon Crisis!) intermittently from 2005-2010; Hoshino contributed illustrations, as well. Each novel was comprised of multiple short stories (eight in total) that expanded the universe of Hoshino's world of Exorcists who fight against the mysterious Millennium Earl & his army of Akuma. Only two stories from Reverse, both from Volume 1, were actually adapted, however, which is disappointing, as the first two books had been fully released by the time the anime debuted on Japanese TV, which would have meant that six stories could have been used.
Anyway, the first story, The Traveling Clergyman, takes place during main character Allen Walker's journey back to Exorcist HQ. In an attempt to find his way back, he visits a woman named Mother for help, as she was once a patron of his master. In return for helping Allen, Mother asks him to help a girl named Riza, who had recently lost a loved one. This story would be adapted into the anime as episodes 29 & 30 under the name The One Who Sells Souls. The second story, The Village Where a Witch Lives, follows fellow Exorcist Yu Kanda as he takes on a mission to recover a group of "finders" who have gone missing in a village which is rumored to be where a witch lives; the story also expands on Kanda's personal search for the character Alma Karma. This would be adapted as episodes 33 & 34 of the anime, using the same name as the original story. Considering how early these two novel stories were adapted into the original anime, it shows that TMS could have really continued adapting stories from D.Gray-man Reverse, but why the studio never did will be something we'll never know. At the very least, those who are filler averse should at least check out these four episodes of D.Gray-man, as they are technically canon to the original story to enough of an extent.
Rurouni Kenshin: Voyage to the Moon World in Rurouni Kenshin
Nobuhiro Watsuki's debut serialization still remains an iconic action manga from the 90s, both in Japan & abroad. That being said, there are two consistent complaints when it comes to the anime side of things for Rurouni Kenshin. The first is that the last story arc of the manga, the Jinchu Arc, has yet to have ever been adapted into anime (minus a short flashback sequence in the Reflections OVA), while the second is that the TV anime adaptation from 1996-1998 really committed seppuku in its last third. While the anime stayed more less true to the manga for the first 62 episodes, it hit a snag once the Kyoto Arc was fully adapted. Still a ratings bonanza, Studio DEEN, (what would later be called) Aniplex, & Fuji TV decided to simply do nothing but "filler" to keep the show on air, which resulted in the show's cancellation after another 33 episodes. In fact, the final episode (which featured a vastly different visual style) was never even aired, instead being a home video-exclusive. That being said, not all of the filler story arcs featured in "Season 3" of Rurouni Kenshin were made up just for the anime. At the very least, I can verify that one story in the anime was taken to some extent from a novel spin-off.
There were two Rurouni Kenshin novels produced while the anime was in production, both of which were written by professional manga critic Kozo Kaku (using the pen name Kaoru Shizuku). The first of which featured a titular story called Voyage to the Moon World, which had Kenshin & his friends help Okuma Daigoro recover a copy of Jules Verne's From the Earth to the Moon, which Daigoro feels holds the secret that can let man actually travel to the Moon, after it gets stolen from him. While I can't exactly judge the accuracy they have to the original novel, episodes 79-82 of the Kenshin anime do feature a Moon-obsessed man named Daigoro, though the story here looks to involve a group of assassins that are after Kaishu Katsu, who is Daigoro's teacher in swordsmanship. These specific episodes were written by Akemi Omode (Meine Liebe, Arc the Lad TV), so there is a fair chance that Omode simply used Kaku/Shizuku's novel story as an inspiration more than anything. The rest of the stories in Kaku's novels are simply retellings of stories from the manga, making this the sole novel "adaptation". Even if it's not exactly among good company when it comes to Rurouni Kenshin episodes, at the very least you now know who to blame if you hated the four episodes taken from this novel short story. Viz did release the entire Voyage to the Moon World novel a few years back, too, so you can legally experience this story in both forms & compare.
Naruto: Itachi's Story as Naruto Shippuden: Itachi's Story: Light & Darkness
About a week ago, it was announced that, this winter, the Naruto Shippuden anime would adapt the three novel spin-offs, Shikamaru's Story, Konoha's Story, & Sasuke's Story, that take place after the main story of the manga ended. These are all part of the Naruto Hiden/Shinden (Hidden Story/True Story) series of novels, which currently total 10. Before these upcoming adaptations, however, was this past spring's adaptation of the two-volume Itachi's Story (which was categorized as a "Shinden") novel. As you may, or may not, have noticed, this entry of the list also uses "as" instead of "in", & that is because the adaptation of Itachi's Story was advertised as its own mini-series, even being promoted as taking the place of Naruto Shippuden for the eight weeks that it ran.
Written by Takashi Yano (Shikamaru's Story, Assassin's Creed 4: Black Flag -Kakusei-), Itachi's Story was originally a two-volume novel (split between Daylight & Midnight) written just last year that acted as extra backstory for one of Naruto's recurring villains, Itachi Uchiha. Starting from when the older brother of Sasuke Uchiha was only four years old & covering up until the Downfall of the Uchiha Clan, Itachi's Story gave a more detailed explanation as to how Itachi grew so cold & distant to his family & fellow Konoha ninja, while also explaining how he gained the skills & allies that he had with him when he debuted in the story proper. With the Naruto Shippuden anime having become intensely infamous for stretching out the final story arc in order to keep it on air for as long as possible (even though the manga has already more than ended), adapting Itachi's Story made perfect sense, so during this past March & April the anime was taken over by this semi-spin-off anime. Technically, this adaptation is still part of the Shippuden anime, especially since it goes off of the existing episode numbering that came before it, but since it was given so much promotion & treated like it's own work, I'll count it in the same way New Fist of the North Star was counted. Viz will be releasing the original Itachi's Story novels at the end of this year, which will be right around when the anime will be adapting those other novel side stories... Perfect timing, I'd say.
The Kindaichi Case Files Novels in Kindaichi Case Files
Still, out of all of the titles I've brought up in this list, the King of Novel Adaptations, though, would have to be Kindaichi Case Files. Written by Yozaburo Kanari (Gimmick!) & drawn by Fumiya Sato (Detective School Q), the murder mysteries that young Hajime Kindaichi, grandson of the famous (fictional) detective Kousuke Kindaichi, are right up there with Detective Conan as possibly the most iconic mystery manga of all time; it certainly adds to the friendly rivalry between Shonen Sunday & Magazine, as well. While the original series only ran from 1992-1997, Kindaich never really ended, with various other manga series taking its place, some of which were written by Seimaru Amagi (a.k.a. Shin Kibayashi), with the most recent being Kindaichi Case Files R(eturns). In fact, R has so far received two seasons of TV anime within the past few years, but before that was the original series from 1997-2000, which ran for 148 episodes; it & R were both aired alongside Conan as a super-popular mystery hour. Even though the original manga was nearing its end when Toei debuted the first TV anime, the staff still decided to not only rely on the manga for content. Luckily, there was already another medium that featured its own set of Kindaichi murder mysteries.
All written by Amagi, from 1994 to 2001 there were nine light novels created that told eight original stories. While the other examples in this list only used portions of their light novel spin-offs, or were simply adapting a single novel, Toei wound up adapting all but the final novel! Let's just simply go in order to cover them all. 1994's Opera House, The New Murder, a sequel to the original Opera House Murder Case, was adapted into the first Kindaichi Case Files anime movie in late 1996. 1995's Ghost Ship Murder Case, which was the sequel to the Lake Hiren Legend Murder Case, was adapted into episodes 28-31 of the TV anime. 1996's Computer Cottage Murder Case was turned into episodes 74-77. Oddly enough, early 1997's Will-O-the-Wisp Island Murder Case was adapted before its predecessor, appearing as episodes 64-67. Late 1997's The Legendary Shanghai Mermaid Murder Case wound up being episodes 90-93. 1998's Thunder Festival Murder Case are what episodes 101-103 adapt. Finally, 1999's Murderous Deep Blue (a two-part novel) was not only originally the second Kindaichi anime movie in 1998, but was also re-adapted into episodes 126-130 in 2000. That leaves only 2001's Heresy Mansion Murder Case, which was never adapted into anything since it came out after the original anime had ended. Of those, The Legendary Shanghai Mermaid Murder Case was also adapted into a live-action movie in late 1997, just a single month after the novel came out.
Without a doubt, the undisputed champion of adapting novels into anime, alongside the original manga, is Kindaichi Case Files.
That brings us to the end of this list of times when anime adapted more than the original manga. Even though "filler" is not always ideal, just remember that, in some rare instances, it isn't really filler at all. Sure, that doesn't always equate to quality, but sometimes you can actually find out where a certain story in the anime came from if it wasn't from the manga, and that's really cool.