This recap begins at the end of the Persona 3 plot.
S.E.E.S: Arisato Minato (Male Persona 3 main character) and Furusato Marina (Female Persona 3 main character) battle Nyx together with S.E.E.S, before sealing it. A month passes with all Persona users forgetting everything supernatural that has happened, until Minato and Marina pass away.
S.E.E.S drift apart and begin pursuing normal lives again.
Persona 4 plot begins.
Investigation team: However, after a few weeks, the Inaba district becomes busy with crime. First Yamano Mayumi and then Saki Konishi are murdered. Souji Seta (Persona 4 Main) discovers the Midnight Channel through rumors, and brings in Yosuke Hanamura. When they work out that somehow the Midnight Channel and the murders are related, they spring into action to save a girl who appears on it. Together, they form the Investigation Team, and work through the next months rescuing and recruiting the characters that are kidnapped to the TV world. Struggling to solve the murder mystery, they work out that only those interviewed on TV are kidnapped and advance the plot of Persona 4.
Canaan subplot: Meanwhile, four teenagers from Inaba are kidnapped in a separate plot, and awaken in a wrecked laboratory complex that they are quick to discover isn't as abandoned as it looks. As they desperately search for the exit, they find themselves being experimented on by a mysterious girl. Old paperwork reveals they have been taken to a human experimentation science laboratory known as the Yggdrasil Institute. In their search for the exit, they accidentally unleash the cosmic horror Hastur from it's depths and are saved only by a heroic sacrifice from the remnants of those experimented on. The four escape.
Investigation team/S.E.E.S: The Investigation Team, having struggled to save many, draw in members of the old S.E.E.S team, causing them to merge and become the IT.S.E.E.S. With S.E.E.S' leaders dead, Souji Seta continues to lead the group unchallenged, and the fresh blood allows them to continue rescuing those kidnapped, but they are still no closer to the identity of the murderer.
Canaan subplot: Persona users unaffiliated with any groups are getting murdered. An actress is arrested 'mid attack', and her younger sister Clarent recruits help forming a group separate and unknown to IT.S.E.E.S, to find the evidence to save her. Clarent is revealed to be a robot created by Yggdrasil Institute.
Using blackmail, she convinces the group to help her destroy a second, still working laboratory: Canaan Branch. They take explosives and break in, and Clarent reveals that she is the true murderer. Her motives for creating the group are to rescue another robot model and kill all other existing persona users. As the group escapes her double cross before the explosives go off, they discover kidnapped teenagers being used as human experiments. They rescue them, and everyone manages to escape just as the explosives go off.
Against the burning backdrop of the building, Clarent fights the leader of the makeshift group one on one and is destroyed. The survivors of the Canaan laboratory join the game and the Canaan plot ends.
Investigation Team/S.E.E.S: The IT.S.E.E.S continue to work. Kinshiro Morooka is found dead, and things get worse. As IT.S.E.E.S try to work out the change in tactics, Mitsuo Kubo appears on the Midnight Channel... Killed by a shadow.
Now on the bad end route, Inaba quickly fills with fog. The fog causes psychosis in the characters over the next fortnight, and shadows begin to emerge into the real world as they grow violent. Only persona users are somewhat immune. Izanami appears on the TV, and IT.S.E.E.S enter the TV world to battle and defeat her. When she is defeated, the knowledge of the fog events fades from NPCs, and the Midnight Channel is no longer dangerous.
Persona 4 plot closes and original plots begin.
Underside Opens: A new place is discovered via portals people accidentally stumble through; The Underside.
Phone / Mask Plot: Armed masked men are already aware of the Underside, and are attacking people. IT.S.E.E.S discover the place, and begin trying to rescue people and fighting the masked men.
A phone in the Underside is heard ringing, followed by special shadows appearing: Shadows reflecting the subconscious fears of the characters. Their worst nightmares in human form roam for a week, before the locked first district of the underside opens, and a phone is found lying on the ground. Arriving at the same time as the masked men, the I.T.S.E.E.S battle them and are defeated. The phone is taken by the masked men, given the masked men some power to control normal shadows.
In the aftermath of their defeat, IT.S.E.E.S take a vote and the winner for leader is the scanner original character Paru. They begin recruiting more help from unaffiliated persona users, and hatch a plan to trap and defeat the masked men. The plan is a success.
Asura Plot: A gang of teenagers arise in Raitou. They have a new ability; they can transform into cannibal demons known as Asura. Their leader, original character Saori, dubs the group Nibelung. Nibelung attacks a member of IT.S.E.E.S. and sparks a series of aggressions between the two groups.
Meanwhile, a variety of spiked drugs begin spreading through the city. These drugs cause insanity in Persona users, and the unfortunate unawakened who take them eventually become Asura, complete with hunger for human flesh. As IT.S.E.E.S. and Nibelung escalate in conflicts, Nibelung discover the underside, and that their hunger for flesh is assuaged by Shadows. The groups manage an unnegotiated period of non-aggression, and attempt to bolster their numbers. Among the recruits, IT.S.E.E.S is joined by Shiba, a persona-using teen, and Nibelung is joined by Ryota, a new Asura.
Eventually, unawakened allies bring it to IT.S.E.E.S' attention that the tainted medicine is the source of the new Asura and the madness gripping some of the awakened. IT.S.E.E.S investigate the source of the spiked drugs at a pharmaecutical plant, and discover ties to the Yakuza. At the same time, Nibelung has a favor repaid by the unaffiliated user Rin, who reveals that the source of the drugs is the Yoshida-kai family of Yakuza.
The Yoshida-kai realize they've been revealed, and decide to destroy both IT.S.E.E.S and Nibelung. Shiba is revealed to be the turncoat assistant of the Yakuza assassin Haru, who the Yoshida-kai have hired. Shiba attacks a member of IT.S.E.E.S at the same time as Haru kills a member of Nibelung; both groups have prominent members of the opposing faction framed for these attacks.
Nibelung launches a counter-offensive, aiming to take out all possible Persona users in the city in retaliation, while IT.S.E.E.S. attempts to hunt down and figure out what has caused this new wave of assaults by Nibelung. Near simultaenously, the Yoshida-kai make a second wave of attacks. Haru attempts and only narrowly fails to murder IT.S.E.E.S. leader Paru. Meanwhile, Ryota ambushes and kills Saori moments after she issued the cease-fire order, after the Yoshida-kai blackmail him into doing so. The remnants of Nibelung are offered amnesty and membership to IT.S.E.E.S. All but one of them accepts; she then murders Ryota, and is taken into custody by IT.S.E.E.S.
The combined forces of Nibelung and IT.S.E.E.S confront Haru and Shiba in the Underside. After several deaths, Haru is murdered by the coalition force, and Shiba is captured by the survivors.
End of the most recent plot. This post will be updated as the next develops.