- Where would Clover have heard of Neostigmine before?
- Who were the three people in the treatment pods before the game began? (Sigma, Alice and Clover seem to be the most likely candidates, but we can't be certain just yet...).
- Why did Zero stop SOIS's raid on Free the Soul's headquarters?
Theme of Nines
- The Mastermind puzzle uses the numbers 1-9 in a random pattern.
- CAS (Cells Alive System) is a real technology, though its actual effectiveness is disputed.
- Sigma's line "you got some 'splainin to do" is a reference to the sitcom I Love Lucy (though Desi Arnaz's character, Ricky Ricardo, never spoke that exact phrase in the show).
Path Summary (Yellow -> Betray -> Green -> Ally)
- Sigma and Phi betray Tenmyouji, leaving their BP at 6 and his at 1.
- Quark falls ill to Radical-6 before being restrained and sedated by the group.
- Sigma enters the Green door with Clover and Quark, ending up at the Treatment Center.
- Quark is placed in one of the pods therein; it cannot cure him, but will keep his condition stable.
- Tenmyouji reveals his identity to Clover, earning her trust; she entreats Sigma to vote "Ally" in the second round.
- Sigma votes to Ally, putting himself, Phi, Clover and Quark at 8 points.
- The group splits up to search for Axelavir in an effort to cure Quark, but ultimately finds none.
- Sigma talks to Clover, attempting to get some information from her. Clover reveals that she works for an anti-terrorist organization known as the SOIS with Alice.
- Alice is revealed to have already been working with the SOIS, investigating the Nonary Game (ruling out that the idea she may be "All-Ice Alice"). After the end of the second Nonary Game, Akane and Santa escaped and, after being questioned and released, Clover later joined the SOIS, and she and her colleagues (fellow Espers from the first Nonary Game) made it their goal to stop Free the Soul. They discerned the location of FtS's headquarters and planned to strike on December 25, 2028; however, Zero's interference prevented this from occurring...
- Clover remembers the effects of neostigmine - it counteracts the effects of tubocurarine. Meaning that it can be used once to allow someone to break the rules, such as, say, going through the number nine door. She quickly leaves the room to inform Alice of this fact.
- Phi seems out of it when Sigma approaches her. Nevertheless, Sigma follows after Clover, finding the much of the facility empty (save for Quark, still in the treatment pod).
- Sigma enters the infimary, finding almost everyone dead (implied to be from Radical-6 infection). Shortly thereafter, Sigma commits suicide as well...
- Clover ending is unlocked.
Beyond Lock #1
- Sigma knows that the injection gun Dio possessed can save one of them from death by tubocurarine. He races to Dio's body and recovers the injection gun.
- Sigma returns to the warehouse just in time for himself, K and Phi to be injected with Soporil.
- Sigma injects Phi with neostigmine, saving her life but dooming himself and K.
- Remembering the plug-key from the GAULEM bay (Magenta -> Ally -> Green -> Ally timeline), he deduces that K removed his armor, leaving it empty on the couch, and snuck off to kill Dio as revenge for killing the old woman. He then returned and re-enclosed himself in it to avoid suspicion.
- K confesses that Sigma's reasoning is correct, and gives him a clue: "If you see a lion with two heads, remember these letters: MIL-KEV-OLI. This will open the second gate."
- Sigma uses the key to remove K's mask; since he is still alive, it comes off.
- K is revealed to be someone who looks identical to Sigma. Before this mystery can be explained, however, both are injected with tubocurarine and expire...
- K ending is unlocked.