Leaving the Q room, the largest computer screen lights up with a username and password. Junpei tries logging in:

Password Lock (username: KURASHIKI, password: JUMPYDOLL (US and Euro) or GRAPEDOLL (Japanese))

Entering the password causes a hologram of Akane Kurashiki to appear from the projector. She greets Sigma and Phi and explains that the game has been played to give them the ability to travel to the past, and to remember things from alternate timelines. Sigma and Phi are confused but acknowledge that this has indeed been happening. Akane also knows that Tenmyouji is with the pair, and points out that he did the same thing in the previous Nonary Game to save a girl's life. Akane promises to meet them both again, and adds, "is the cat in the box alive or dead? It's up to you."

All three leave the Q room. In the warehouse, Tenmyouji suggests that Phi should vote alone in the AB Game, since being on 9 points she has no benefit from betraying. Phi finds this acceptable, but the others decide not to vote straight away, since they would be stuck in the AB room for 45 minutes. The others head off to look after Quark and Alice, while Sigma and Phi remain behind. Phi states that she believes another jump is coming up, and that it will have something to do with rescuing Akane.

TO BE CONTINUED appears, and a new location appears on the Flow map at the very top. Choosing this new location has Sigma and Phi re-appear in the Elevator.

Sigma wakes up in the Elevator as at the beginning of the game, and doesn't recognise Phi. But this time, Phi immediately says that it's not an elevator at all but an AB room, and Sigma remembers the game and who Phi is, and why they are there. Looking at their bracelets, they realise they have woken up slightly earlier than they did on their first play of the game, and Phi says they should hurry up and escape to try to save Akane.

SEEK A WAY OUT: this behaves like the original Elevator Escape, but you can't interact with anything except the safe (Phi will tell you that you don't need to). Entering the escape password, which you already know, reveals the key and this can then be used to reveal and push the red button and leave. (Entering the file password reveals an empty safe and Phi tells you off.)

Sigma and Phi jump out of the top of the AB room and see Akane standing in the warehouse, and Dio sneaking up behind her with a knife. Phi jumps from the top of the AB room and drop-kicks Dio in the head, knocking him out cold. Akane turns and welcomes the pair, congratulating them on finding her, and on the abilities they have developed, and thanks them for saving her. She explains that she doesn't have a lot of time, because she needs to reset the game to the proper starting condition before Sigma and Phi are due to wake up from their original jump, or "very bad things will happen". Sigma is shocked that Akane would set up a game that would result in her, Sigma, and many others dying, but Akane explains that this was necessary for the main purpose of the project, and that thanks to Sigma in the current timeline no-one will die.

Akane gives Sigma a key, marked with the legend "tu fui ego eris", and ties it around his ankle. She calls out, "Lagomorph", and the Zero AI appears. She commands him to unlock her bracelet, and he immediately does; she puts it on the unconscious Dio. She explains that Sigma and Phi are about to jump out again, and that she will put them back into their AB room and reset the puzzle so that no paradoxes will be caused. She also suggests that he meet her again, using the key she has given him, and then Sigma jumps out again.

TO BE CONTINUED appears, and a new location appears at the very bottom of the Phi branch. Choosing this new location has Sigma wake up in the Infirmary.

Sigma wakes up in the infirmary surrounded by the other players. They explain that he's been unconscious for more than an hour, but breathing, and they've only just brought him round. While he was out, they have been using the remaining bracelets to play the AB game and Allying every time, so everyone now has at least 9 points. Sigma is amazed at this feat of trust and realizes that it may have occurred because nobody has died or needed to do anything that might break trust in this timeline.

The entire group (except Dio, who they decide to leave behind) leave through the number 9 door, pass through the Pressure Exchange, and head outside. Nobody knows which desert they might be in, but then Tenmyouji announces that he knows where they are, and when it is. He explains that it is 2074, and that 45 years passed between their kidnapping by Zero and the start of the Nonary Game. Shortly after Sigma was kidnapped, the Radical-6 virus escaped from a mars mission simulation being conducted in Nevada, and become a pandemic. Many people killed themselves, or died from the breakdown of society that occurred when others did so. Finally, a group of survivors decided to attempt to exterminate the virus completely by detonating all of Earth's 14 annihilation reactors. This blasted dust into Earth's sky and devastated the planet. Tenmyouji is unsure if this was a genuine attempt to kill the virus or just the effect of Radical-6 on those particular people. The red planet in the sky is not the eclipsed moon: it is the Earth, which appears red because of the level of dust in the atmosphere. The players are on the moon.

Sigma says this can't be the case, as he would have noticed the differences in gravity, and Tenmyouji points out that they did: Sigma and Phi both mentioned their bodies felt different. Also, everyone is infected with Radical-6; since their brains are operating more slowly, they percieve things falling faster than they actually are, so although items are falling more slowly in the lunar gravity, people aren't noticing that. That's also how Phi was able to "fly" and jump so high: they're in lunar gravity.

Sigma announces that he needs to go back and meet someone important, and the others re-enter the facility through the large door on floor B, which can be opened normally from the opposite site. Sigma leads the others to the botanical garden, and uses the key to open the grave, which causes a further treatment pod to emerge from the ground. Sigma explains that he believes Akane is in the pod, and tries to open it, but it won't open - a moment later the computer announces that the pod is beginning to defrost, and Sigma realizes the pod has been sent to cold sleep and will take a while to thaw out.

K then announces that his memory has fully returned. He grew up in the facility, and the old woman and Zero both created the Nonary Game as a project to enable Sigma and Phi to learn to send their bodies back in time. The game was designed from the ground up to do this. Infecting the players with Radical-6 to cause their brains to slow down would cause greater "potential" to build up in Sigma and Phi's brains over time. Solving puzzles would strengthen their connection to the fourth dimension, and the moments of crisis in the game would potentially trigger jumps. The game was designed to have many choices and options in order that there would be many timelines between which Sigma and Phi would jump. The eventual goal is that they should be able to jump back in the past to before the Radical-6 outbreak happened, and prevent it from happening.

The pod completes defrosting, and everyone stands around as it opens: but the person inside is not Akane, but a clone of Sigma. Sigma and Tenmyouji are both baffled, and K apologises and reaches up to release his helmet, revealing that K is Akane Kurashiki. Akane explains that she was not always in the K armor; after Sigma and Phi saved her, she got into the armor and put the original K into cold sleep, in order that the game could continue with her present without causing any paradoxes. She's created a Schroedinger's Cat situation: the person in the armor, K or Akane, is determined by Sigma and Phi's future actions.

Clover and Alice ask why it was necessary for the other players to be dragged into the game if it was really about Sigma and Phi. Akane replies that they all had roles to play. Clover is an esper, meaning that her presence could enhance the strength of other espers present; so is Tenmyouji. Tenmyouji insisted on bringing Quark with him, not knowing that he was entering a Nonary Game. Alice was necessary since she had the skills necessary to decode Dio's message in one of the timelines, which was in turn necessary to disarm the bombs. Luna is a GAULEM who is helping the players get through the game. Dio was not invited to play the game, but broke in at Brother's command to sabotage it: nonetheless his presence was necessary to create crises that would enable Sigma and Phi to jump.

Akane asks if anyone recognises the man sleeping in the pod, and everybody declares they have never seen him before. Sigma is confused, pointing out that they both have the same face, and Clover asks if he's quite alright. Akane explains that Sigma's consciousness can jump to the past, but as a result, he can also be jumped to the future. Sigma rushes over to look at his reflection in the pool, and is shocked to see that he is now an old man wiht a cybernetic eye. "Zero Sr, the mastermind of the Nonary Game.. is you."

Akane explains that he is Doctor Sigma Klim. Sigma announces that he isn't a doctor, and Akane replies that in the future, he will be. Sigma and Phi's ability to jump to the past has been demonstrated by the game, in circumstances of high mental potential and crises: and at that moment, Akane draws the Myrmidon's knife and charges at Phi. Sigma rushes at her to stop her, and then begins to fade out, only dimly aware of Akane's body lying on top of his. As he fades, his last view is of the words "tu fui, ego eris" on the grave: "what I am, you will be. What you are, I will become."

PHI: END appears and a new location is added to the Flow at the very top. This new location plays END or BEGINNING.

On the PS Vita version, getting this ending gives the achievement Time After Time.