- "Nijisaki was his right-hand man, and did the lion's share of the planning."
- — Snake, explaining Nijisaki's role in the First Nonary Game
Nagisa Nijisaki (虹崎 渚 Nijisaki Nagisa) was one of the four Cradle Pharmaceutical executives responsible for creating the First Nonary Game. He was the right-hand man of the CEO of Cradle Pharmaceutical, Gentarou Hongou, and Cradle Pharmaceutical Chief of Staff.
Nijisaki wore a purple suit, as seen in the only photograph showing his past self. He had a rose attached to his left breast pocket and wore a gray tie. His hair was described as kind of long by Junpei. During his time in the Second Nonary Game, he was forced to wear Snake's clothes in order to confuse Ace, since Ace had prosopagnosia.
His personality is unknown, since he was never spoken to, but during the Second Nonary Game, he was drugged so he could not speak or defend himself. To Junpei, he looked smart, yet a little cold.
Although not shown in the game, Nagisa Nijisaki is one of the people who killed Akane Kurashiki in an alternate history, implying he is twisted similarly to Gentarou Hongou, which could justify her indirect murder of him.
At the time the First Nonary Game was planned, Nijisaki was the one who was part of the planning of the First Nonary Game. Overall, he was the one who had put together Hongou's designs and was the man working under him.
Nine Hours, Nine Persons, Nine Doors
During the Second Nonary Game, he too was unknowingly abducted, drugged, and placed in Building Q in Nevada by Zero, presumably somewhere the other players had no access to at the time. He was forced to swallow a small bomb. It is implied Nijisaki is also a Free the Soul member, which is why he was wearing ceremonial robes which originally belonged to Lord Dashiell Gordain.
During the time the 8 players were looking for the missing components of the RED device of the large hospital room, Nijisaki was drugged by an unknown person, who was probably Santa or June and presumably also using gaseous Soporil. Nijisaki had his clothing swapped with clothing belonging to Light, who went under the codename Snake, which of course, had Snake feeling soporific and knocked unconscious dressed in ceremonial robes belonging to Lord Dashiell Gordain, beforehand, and placed in the coffin in the chapel. Nijisaki was placed in the big hallway that connected to the large hospital room, wearing a number 2 bracelet just like Light.
While he was walking towards the large hospital room, Nijisaki had the misfortune to encounter Hongou, who was known as Ace by the players of the Nonary Game. Due to his past with Snake, Hongou attempted to kill who he thought was Snake but failed to realize that he was actually Nijisaki due to his prosopagnosia.
With the number 2 bracelet placed on Nijisaki's wrist, his own bracelet, and the bracelet taken from Teruaki Kubota, who was known as the 9th Man by the players, Hongou was able to open Door 3. Under the assumption Nijisaki was Snake, he shoved him past the door. From there, Nijisaki had the bomb inside him activate like Kubota, who shared the same gruesome death.
- "What was left of the body sat in a sea of blood. Chunks of flesh, torn from the body, sat in the blood like tiny islands in a great, red sea. A vast, ragged hole had been torn in the torso, and what remained of his intestines spilled out of it like fresh spaghetti. Smaller chunks of meat had splattered against the wall, and become stuck there as they dried. Globules of yellowish fat had left trails like tiny slugs as gravity pulled them down the wall, even as they dried to it."
- "It looked as though the explosion had been quite powerful. His legs were both bent in an odd, unnatural way, and his left arm had split open, exposing the painfully white bone of his ulna. His bracelet lay next to him. It seemed to have hit the wall hard enough to have shattered the display, which lay on the ground in pieces. Half of his head had simply collapsed. The blood coating almost made it look like raw pizza dough covered in tomato sauce. His clothes, too, were covered in blood. The burgundy tie, the white shirt, the jacket with the yellow piping, and the gray slacks... They were all familiar to Junpei."
- "The only thing on the other side of the divider was a dead body, lying in a reddish-brown puddle of dry and drying blood. There are many ways a man can die, but this... The skull was shattered, and the head little more than a pulpy mass of brain, bone, and viscera. The left arm was hideously twisted into a horrific, alien shape, the bright white of the ulna shining through the remains of skin and muscle."
When Hongou, Clover, and Seven entered Door 3 (more specifically, the shower room), they had stumbled into the remains of Nijisaki's explosion, which scared Clover into thinking Snake was dead and caused her to become depressed. Once they solved the puzzle of the shower room, they came back into the large hospital room only to conveniently stumble onto Junpei, Santa, June, and Lotus, who were exploring the central staircases and the areas they could enter using the keys found in the operating room and laboratory. Soon, they showed the four of them the remains of Nijisaki's (although throughout most of the Second Nonary Game, he was still presumed to be Snake due to his clothes) body after his explosion.
During the players' discussion about how Snake's death played out, it was hypothesized that he had died just like Kubota. To Seven, the killers (it was required for at least 3 people to open a numbered door) and Snake authenticated to open Door 3 and once the door opened, the killers pushed Snake inside Door 3 and waited for the door to close. Once it did, Snake had tried to find the DEAD in the shower room, but since it required all of the people who opened the door to authenticate at the DEAD to deactivate the bomb, Snake's attempt didn't work and he ended up exploding in the shower room. It was presumed that Snake had died during the time they were looking for the missing parts of the RED.
Ace shrugs it off since he thought that it was Zero's doing that Snake had died and the idea of multiple killers was just there to make them fight among each other. Clover, who was grieving and traumatized from the death of "Snake", suggested that Zero is one of the remaining players. Junpei agreed with Ace's and Clover's theories that Zero had to be the one who killed Snake but Lotus managed to debunk his argument when the question of why Zero would hide as one of them arouses, as they were unaware of Zero's true motives.
Later on in the chart room of Door 1, Clover asked Junpei who did he think killed Snake. Although Junpei thought it was Santa and Seven (3+7+2=12, 1+2=3) since it was the only combination of 2 people that could work, he suggested that there were other possibilities for the killers. Clover then wrote on Junpei's notebook and showed him the only 8 combinations that would work, assuming that it only consists of the players who were currently alive. 7 combinations were crossed off though since it consisted of Clover, June or Junpei, leaving only the following combination: 2+(1+3+7+8)=21. Since it made everybody except for Clover, June, and Junpei working together, it was deemed unlikely that 3 or 4 persons were the killers.
Soon after Ace, Clover and Junpei found Kagechika Musashidou dead wearing clothes of a captain in the captain's quarters, Clover and Junpei discussed about how Musashidou (nicknamed Cap by Junpei) couldn't have been Zero since it was too obvious. When Junpei remarked how Cap had it better than Snake when he died since he was killed with an axe instead of exploding, he accidentally mentioned Snake's left arm had a broken bone sticking out of his left arm. Soon, Clover started crying and she revealed that the dead body inside the shower room wasn't Snake since his left arm was a prosthetic one.
Sometime later in the chapel with the two Door 9s in it, Junpei, Clover and Seven spotted a coffin shaking. Junpei hears the "sinister hand" voice in his head, heavily implied to be June communicating to him. Using logic, Junpei inserted "14383421" in the lock and the coffin was unlocked. A couple of seconds later, Snake emerged out of it, showing that the dead body in Door 3 wasn't Snake after all. Clover started crying out of joy and embraced her brother. Snake told the three of them that he was gassed in a small room in one of the hallways of C Deck using the same method Zero used to abduct all of the nine players. Seven quickly summarized the events they had occurred after Snake went missing: two people had pushed Nijisaki (who was called Guy X) into Door 3 after they had authenticated on the RED.
In the library, Snake told Junpei about the Nonary Game and the four executives of Cradle Pharmaceutical who organized it. One of them was Nagisa Nijisaki, the CEO's right-hand man. When Junpei, Snake, Seven, and Clover found the picture of the four Cradle Pharmaceutical executives in the study, he was revealed to be Nagisa Nijisaki.
In the incinerator, Junpei explained to the weakened Ace how he had killed Kubota, Nijisaki, and Musashidou.
- The first syllable of his surname is the Japanese word for "two", referring to him being killed in place for Snake.
- He is one of three characters to die regardless of the ending in 999. The other two are Teruaki Kubota and Kagechika Musashidou.
- A plot contrivance is that for some unknown reason, Hongou failed to differentiate between Light's and Nijisaki's hairstyles and hair colors. This could easily be fixed by Nijisaki wearing a wig.
- Another plot contrivance is that Nijisaki never spoke for some unknown reason. It is implied in-game that Nijisaki was extremely dazed by Soporil.
- Like Kubota, it is unknown if Akane planned the Nonary Game with the intention of Nijisaki dying. However, considering the clothes swap and Hongou running into Nijisaki, it is likely she did.
- A trailer for the game said "9 kidnapped strangers" and "9 unwilling participants". This is likely a nod to Nijisaki and Musashidou who are included as being kidnapped and unwilling participants, while Akane and Aoi are not as they are not kidnapped and they are willing participants.