Having graduated from the Academy, Shikamaru was first seen in the anime to be surprised by Naruto's graduation despite the latter failing the graduation exam. He was later assigned to Team 10 along with Chōji and Ino, who said moments earlier that she would not want to work alongside someone as lazy as Shikamaru, much to his amusement.
Shikamaru, along with the rest of the Rookie Nine, participated in the Chūnin Exams, commenting that it was "such a drag" that they were up against many candidates. During the first phase, Shikamaru had already figured out the true purpose of the written exam and was glad that Ino had figured it out as well when she used her Mind Transfer Technique on Sakura.
During the second phase of the Chūnin Exams, Team 10 stumbled across Sakura Haruno being attacked by some Oto genin. Although he said he didn't want to get involved, Shikamaru dragged Chōji along once Ino joined the fray. The team then initiated the Ino–Shika–Chō battle formation, Shikamaru immobilising Dosu Kinuta. Soon after, Sasuke Uchiha awakened, his newly received Cursed Seal activated. As Sasuke prepared to attack the Oto genin, Shikamaru told Ino and Chōji to join him in abandoning their roles in the battle as Sasuke's onslaught ensued.
In his preliminary battle, Shikamaru fought against Kin. He defeated Kin by sneaking his shadow under the thin strings she was using to control her bells; she did not notice that a string that thin and that far from the floor could even make a shadow. Shikamaru then took a shuriken from his pouch, with Kin, caught in his Shadow Imitation Technique, doing the same thing. Because of Kin's increased proximity to the wall of the arena, she knocked herself unconscious as Shikamaru ducked under her projectile.
In the anime was shown that he trained to the final round with Chōji. When the latter was hospitalised due to eating too much, Shikamaru brought him a basket with fruits, but Chōji was forbidden to eat it. Shikamaru then found out that Naruto Uzumaki lied at the hospital as well and when the latter waken up the two encountered Gaara who was about to kill Rock Lee. Gaara told them about Shukaku sealed within him and tried to kill them, but he was stopped by Might Guy's arrival.
One day before the final round Chōji overheard Guy and Naruto talking about the "Fourth Hokage's legacy". Chōji then told Shikamaru and Ino about this. Later Naruto and Sakura met with Team 10 at the entrance. They ended up teaming up with Sakura and Naruto to find the "Fourth Hokage's Legacy". Through out their adventure Shikamaru showed his intellect solving multiple puzzles and ending up saving the other four multiple times. In the end he decided to give the "Fourth Hokage's Legacy" to Naruto realising that as long that someone from the Konoha gets it it will be ok. However, they realised that this whole mission was made up by Guy and, partially, by Kakashi as a sort of extra special training.
In the final round, Shikamaru was matched against Temari, where it initially seemed as if he was just pointlessly attempting strategy after strategy. Temari assumed that he was simply buying time for the sun to set, furthering the range of his shadow. He was in fact manipulating her into a position in front of the exit to a tunnel which was dug out by Naruto during an earlier match, where he could guarantee that she was caught by his shadow from behind. However, after Temari was actually caught in his shadow imitation, he then simply forfeited the match, claiming to have spent too much chakra to proceed with any additional matches. Moreover, he said he did not like to hurt or hit women. Despite having forfeited, Shikamaru's brilliant strategy impressed everyone, including the Hokage.
When the invasion of Konoha began, Shikamaru was able to dispel the genjutsu that swept through the stadium, though he pretended to be asleep to avoid taking part in the battle. Sakura noticed this and forced him to help in pursuing Sasuke. As they pursued Sasuke, they discovered that nine Oto ninja were following them, and Shikamaru chose to stay behind so he could stall them while the others continued to follow Sasuke. Using a clever strategy, he was able to trap eight with his shadow. However, the ninth Oto ninja hid in the trees, protecting the captured eight against Shikamaru's attacks. Despite discovering the ninth's hiding place, he could not fight off the Oto ninja, after being drained from his earlier match against Temari. Asuma arrived in time to save him, and defeated all nine Oto ninja single-handedly. Shikamaru is later seen attending the Third Hokage's funeral.
Because of his performance during the Chūnin Exam finals, Shikamaru was the only genin that was promoted to the rank of chūnin. Shikamaru was given his first assignment of forming and leading the Sasuke Retrieval Team to stop Sasuke from defecting from the village. Because Konoha suffered heavy casualties during the failed invasion by Sunagakure, Shikamaru was forced to limit the members of his team to genin. He immediately recruited Naruto and Chōji, and then added Neji and Kiba to the team. Upon setting out, Shikamaru formulated a plan on how to approach Sasuke's escorts, the Sound Four. Their presence was detected, and they were trapped by Jirōbō. However, Shikamaru was able to find a way to escape. He was ultimately forced to leave Chōji behind to fight Jirōbō, but had no concerns that Chōji would lose, and marked the team's path so that Chōji could follow them.
The team continued to break apart, one member of the Retrieval Team engaging one member of the Sound Four. To give Naruto a chance to go after Sasuke, Shikamaru fought Tayuya. Tayuya summoned three demons, that she controlled with her flute and easily gained the upperhand against Shikamaru. Counting his remaining weapons, Shikamaru devised an elaborate plan. He threw eight kunai at Tayuya to see what finger movements she would use to protect herself with. Being unable to read her music he eventually took control of the three with his shadow, telling her how he found shogi fun because he could take over his opponent's pieces. Shikamaru then attacked with the three demons prompting Tayuya to remove the demons but she was still caught by his shadow. By activating the second stage of her cursed seal, Tayuya was able to resist Shikamaru's shadow.
Picking up a kunai that had missed her earlier she tried to slit his throat but was suddenly punched in the gut and caught by his shadow again, revealing that he only pretended to fall prey to her genjutsu, as he had used his shadow to break his finger to escape it. Shikamaru then explained about his plan and how he missed with that kunai on purpose to get her close while he then prepared his Shadow–Neck Binding Technique. As he was about to run out of chakra, he was saved by Temari. After Shikamaru gave her a tactical update she blew away her sound based genjutsu with her wind and then used a summon to finish her off.
Temari accompanied him back to Konoha, where they learned that Sasuke had escaped, and that everyone on the team suffered injuries despite being helped by Temari's two siblings, Gaara and Kankurō. Shikamaru's initial reaction to the failed mission was to quit being a ninja altogether, but his father scolded him for being such a coward, explaining that his friends would then only be led by some other ninja. If they were to die under that ninja's command, Shikamaru would feel worse for not having been there to try and save them. When he was informed that everyone on the team would make a full recovery, Shikamaru cried out of joy and relief, and resolved to do better next time.
He later saw Temari and the Sand Siblings off and, in the anime, was appointed as an Academy instructor.
Two and a half years later, at the beginning of Part II, Naruto ran into Shikamaru and Temari soon after returning to the village. Naruto initially thought that Shikamaru and Temari were a couple, although both denied this, explaining that they were working on planning for the next Chūnin Exam. This later prevented him from helping with Naruto's first attempt to look for Sasuke, but he was able to help during Naruto's brief scuffle with Sai.
In the anime, when Konoha was invaded by Furido and his team, Tsunade put Shikamaru in charge of Konoha's defence. He grew frustrated that his friends were fighting on the ground while he was on the back lines. Shikamaru stated that a strategist must lead his troops from the front line, and not be afraid to take risks. After getting Ino, Shikamaru led the counter-attack against the undead, ordering an attack plan which drove the enemy back. Later, Shikamaru used his Shadow Imitation Technique to bind Sora.
Shikamaru was revealed to be a member of the Nijū Shōtai, where he was teamed up with Asuma, Izumo Kamizuki, and Kotetsu Hagane in an effort to track down and eliminate any and all members of Akatsuki. Eventually, the team found one such member: Hidan, and, as Shikamaru restrained Hidan with his Shadow Imitation Technique, the rest of the team were able to co-ordinate a finishing attack on Hidan. When it was revealed that had done little to stop Hidan, Hidan's partner, Kakuzu, appeared, forcing Shikamaru to release Hidan.
As Asuma battled Hidan, Hidan began a ritual that caused all damage done to himself to be inflicted on Asuma as well. Because of Hidan's apparent immortality, Hidan was able to use this to his advantage, giving himself injuries to easily harm Asuma while not being affected by the debilitating blows himself. To help Asuma, Shikamaru captured Hidan with his shadow once again, and adopted his meditative analysis of all of Hidan's actions and words up to that point. He quickly realised that the "link", created when Hidan consumed Asuma's blood, could only be maintained by Hidan remaining within the blood seal that he had earlier drawn on the ground, so Shikamaru pulled him out of it. With damage done to Hidan no longer harming Asuma, Shikamaru tied Hidan down with his Shadow Sewing Technique, allowing Asuma to decapitate the Akatsuki member.
However, even this was not sufficient enough to kill Hidan. After Kakuzu reattached his partner's head, he joined the fight and pinned down Izumo and Kotetsu, while Hidan managed to bind Asuma to his curse jutsu again by stepping back into the blood seal. Shikamaru rushed to the aid of his sensei just as Hidan impaled himself with his spear, delivering the final blow to Asuma. Chōji and Ino arrived as back-up, and Hidan and Kakuzu were driven off. Ino tried to heal Asuma, but there was nothing she could do, and the students were only able to listen to Asuma's final words. To Shikamaru, Asuma said that he had great potential, perhaps enough to one day become Hokage. After Asuma died, Shikamaru began smoking his first and last cigarette, blaming its smoke for his tears.
Shikamaru did not attend Asuma's funeral, instead coming up with a plan to defeat the Akatsuki duo. This was drawn out considerably in the anime, where his father made an attempt to comfort him with a game of Shogi, though Shikamaru could only blame himself and was too invested in revenge. When he finished his preparations, he set out with Ino and Chōji. They were stopped by Tsunade, who insisted that they stick to the usual four-man team. Kakashi appeared, and volunteered to help, so Shikamaru quickly modified the plan to accommodate for his presence.
Upon finding Hidan and Kakuzu, Shikamaru used Asuma's trench knives, swelling with his shadow, to restrain the Akatsuki members by pinning their shadows. With the two unable to fight back, Shikamaru prepared to trap the two with his Shadow Imitation Technique to allow him more of an advantage, though Kakuzu was able to escape before Shikamaru could ensnare him. With Hidan under his control, Shikamaru used Hidan to attack Kakuzu, forcing him into a corner where Kakashi attacked him with his Lightning Cutter. This destroyed only one of Kakuzu's four extra hearts, and, surprised by this turn of events, Kakashi and Team 10 regrouped. After being left on the defensive for a while, Shikamaru concluded that they must separate Hidan and Kakuzu if they were to win. To this end, Shikamaru again caught Hidan with his shadow, and led him away.
Once far enough, he covered the area in explosive tags to corner the immortal. The time limit on his Shadow Imitation then ran out, so Hidan was able to attack him, get some blood, and initiate his ritual. Hidan quickly stabbed himself in the heart, causing an apparently dead Shikamaru to keel over. Shikamaru was, however, alive and well; the blood had been Kakuzu's, Kakashi having taken a sample when he earlier used Lightning Cutter. In effect, Hidan stabbed Kakuzu in the heart. With Hidan oblivious, Shikamaru tried to decapitate him with a short sword. The cut was too shallow to sever the immortal's head, prompting Shikamaru to capture him in a Shadow Imitation instead - albeit a much weaker one at this point, with his chakra running low.
As Hidan tried to attack Shikamaru, Shikamaru used his Shadow Gathering Technique to cover Hidan with the explosive tags in the area. With Hidan tied in place, Shikamaru activated a mark he had prepared before the battle, causing the ground beneath Hidan to collapse into a pit. Hidan cursed at saying once he was free he would kill him, but Shikamaru explained that the surrounding forest was the property of the Nara clan; only they were allowed to enter or leave the forest, thus ensuring that Hidan's remains would never be found while one of his clan's deer, Rikumaru watched on. In the anime, after lighting a cigarette, Shikamaru flicked Asuma's lighter at Hidan, setting off all of the explosive tags at once. Hidan's remains fell into the pit and, as he swore vengeance against Shikamaru, Shikamaru forced a cave-in. With the battle won, he regrouped with his team escorted by Rikumaru, Kakuzu having also been defeated by Naruto, and returned home. When he got back, Shikamaru stated to Kurenai that it is now his ambition to protect and train the next generation of ninja.
Shikamaru was left in charge of deciphering Jiraiya's dying message about Pain. When informed by Shiho that the Konoha Cryptanalysis Squad couldn't break the code without some sort of key, Shikamaru approached Naruto for help. Using his own experiences with Asuma's death, he helped him to get over Jiraiya's death, pointing out that they would someday both have students, and would also go to great lengths to protect them, just like Asuma and Jiraiya. Revitalised, Naruto helped to decipher the code which revealed the message: "The real one is not among them." Shikamaru proceeded to figure out what this meant, but was interrupted by Pain's invasion of Konoha.
In the anime, Shikamaru immediately goes to check on Kurenai, arriving in time to kill the Giant Centipede attacking nearby. He then helped Kurenai to an underground passage to evacuate. After the village's destruction, he and his father were shown to have survived, although Shikamaru received a broken leg when he shielded Shiho from harm. They regrouped with Ino and her father, and pooled their knowledge of Pain to try and figure out his secret. They discovered that Pain had a main body that must be nearby, so Inoichi and Shikaku went looking for it. Because his leg made it difficult to move, Shikamaru stayed behind, later joining in on the celebration of Naruto's victory over Pain.
During Iruka's flashback of Naruto as a young prankster, Shikamaru was shown to be curious as to why Naruto was hated by the majority of the village. At one point he and Chōji wintessed a shopkeeper assaulting Naruto while the latter was harmlessly browsing for a face mask. Seeing everyone glaring at Naruto with hostility, Shikamaru asked his father why Naruto was viewed like a disease. Shikaku did not answer his son's question but told him to follow his own feelings. When Shikamaru and Chōji next saw Naruto heading off to the back hills on a dare of three boys, he remembered that a battle had taken place there quite recently and bearing no hostility towards him, tipped Iruka off of the danger Naruto was unknowingly walking into.
Back in the present Shikamaru, along with Shiho, was looking at a table filled with salvaged photos of villagers. They were trying to sort them out to give them back to their rightful owners.
Shikamaru remembers a time when Team Asuma, along with Team Kakashi, went on a mission where they had to save a Village Headman's granddaughter from a gang boss named Baji. After analysing the situation, he recommends Kakashi and Asuma to take an alternate route to the boss' fortress. After infiltrating the boss' fortress, he agrees for a hostage exchange between himself and a man named Tōfu. He is then taken up to a secret room where the Headman's granddaughter is being kept. Moments later, Ino and Chōji catch up with him, apprehend Baji and save the girl, completing their mission.
When news reaches Konoha of Sasuke's recent dealings with Akatsuki, Team 10, Team 8, and Team Guy decide that they should personally kill Sasuke before he involves the village in a war. Shikamaru volunteers to approach Team 7 on the group's behalf and inform them of their decision. Sakura reluctantly agrees with him. Because Naruto is in the Land of Iron, Sakura offers to tell him for Shikamaru. When Naruto returns to Konoha he meets with Shikamaru and the others to tell them he understands their reasons, but asks that dealing with Sasuke be left to him.
Shikamaru and his father attend a war council to discuss the village's preparations for the looming Fourth Shinobi World War. Although Shikaku believed his son too young and inexperienced to be there, Shikamaru resolved to use every brain cell he had to memorise everything during the meeting. In the anime, before attending the meeting, he sees Naruto being chased by Konohamaru and he can't seem to get Naruto and the Nine-Tails out of his mind and remembers of what Hinata and Yamato said to him earlier, resolving to doing everything possible to protect him.
When the war begins, Shikamaru is placed in the Fourth Division alongside Chōji. Although Gaara is technically the commander, Temari tells Shikamaru that, as Gaara's proxy, he is effectively in command. Shikamaru, Chōji, and other members of their division are later sent to provide support for the First Division. They meet up with Ino - sent as backup from her own division - and they team up to help Darui fight Kinkaku. Shikamaru restrains Kinkaku with his shadow but only barely holds him long enough for Ino to use the Mind Body Switch Technique on Kinkaku, leading to Kinkaku's capture within the Kohaku no Jōhei. Ino–Shika–Chō next engages the revived Kakuzu. As they prepare to face him yet again, he points out that he is not the only ninja to have been revived: Asuma is on the battlefield too.
As Asuma's students and thus experts on his fighting style, Shikaku leaves fighting him to Ino–Shika–Chō. Shikamaru goes after Asuma with his shadow to create an opening for Chōji to attack him, but Chōji is reluctant to attack their late teacher. While Chōji struggles to find his resolve, Shikamaru tries to hit Asuma with his Shadow Imitation Shuriken Technique. Asuma blocks it with a kunai and goes after Chōji, forcing Ino to transfer her consciousness to Chōji's body and fight for him. Shikamaru looks after her unconscious body, using his shadow to make it imitate defensive actions against white Zetsu. With encouragement from Shikamaru, Ino, and even Asuma, Chōji finds the resolve to fight. Shikamaru again uses his shadow to create an opening, allowing Chōji to fling Asuma into a cliff wall. Shikamaru pins him there with Asuma's old Chakra Blades. Defeated, Asuma congratulates them on their perfect teamwork before being sealed.
The battle continues into the night and Shikamaru assists Chōji in mopping up the rest of the revived ninja. Before they can claim victory, Tobi appears on the battlefield with the Demonic Statue of the Outer Path. While the Statue wreaks havoc, Tobi goes after the Kohaku no Jōhei and the Benihisago. Remembering information given to him by Temari about the Statue and the tailed beasts, Shikamaru deduces that Tobi plans to use the brothers' Nine-Tails-chakra. Tobi calls Shikamaru a worthy adversary for figuring out what he had planned and has the Statue attack him. He is saved by Chōji while Tobi escapes with the brothers. After the attack subsides, Shikamaru is seen planning with the rest of his team and Tenten.
The next day, in order to counter the mayhem of the White Zetsu Army clones that had infiltrated their ranks until Naruto arrived to differentiate them, Shikamaru has everyone draw circles around themselves that they were not allowed to leave or enter another one. When Ino asks him if they couldn't just ask questions to confirm each other's identity, Shikamaru tells her that's there too big a chance that an enemy could simply guess the right answer. He later tells Dan who Naruto was and his dreams of becoming Hokage after Dan initially mistakes him for Nawaki.
After being informed by Inoichi from HQ that Naruto and B were fighting the "masked Madara", Shikamaru and the rest of the Konoha 11 rush to his aid. As he runs, he tells Chōji that he'd expect nothing short of Naruto overdoing things on the battlefield and because of his short temper, he wasn't one to calmly think a plan through, so Naruto should wait for him.