I am basically going to be giving comparisons as to what was better in which game.
Part 1: Story
P3The JourneyPersona 3 begins with the Main Character returning to the
city after ten years. He is quickly brought into SEES when his
awareness of the Dark Hour is revealed and that he can summon multiple
Personas into battle. With their help, SEES is able to explore Tartarus
further and defeat Greater Shadows that appear every full moon,
believing that by killing all twelve of them, they will be able to end
the appearance of the Dark Hour. However, SEES learns they have been
misled; by destroying the Greater Shadows, they have freed parts of a
being called Nyx who will bring about the end of the world if it is
fully restored. It is revealed that the Kirijo Corporation was
attempting to do this ten years ago, but Nyx was released prematurely
in a laboratory accident that also created the Dark Hour and Tartarus.
Aigis, a robot designed to fight Nyx, battled the being but was unable
to fully defeat it, instead dispersing parts of it into the Greater
Shadows, and installing the last part into that of a young boy nearby,
revealed to be the Main Character.
SEES encounters Ryoji, a teenage boy who tells him he is Death
incarnate and that he will unwillingly usher in Nyx and the end of the
world. The player is given the option to kill Ryoji at this point; if
taken, the game explains that members of SEES lose memories of the last
year, and show them leading normal lives until inevitably the end of
the world occurs. If Ryoji is spared, then the game continues, and on
January 31, SEES climbs to the top of Tartarus to face Ryoji, now in
his true form of the avatar of Nyx. Though they defeat it, the avatar
is still able to call forth Nyx; the moon splits open revealing a
strange device that begins to kill people across the Earth. The Main
Character uses all of his Social Links gained from SEES and other
friends to create a seal to lock Nyx away, though sacrificing himself
to do so.
The world returns to normal, though the memories of the past year
are lost to the SEES members. As they finish school, they come to
realize that they each promised to gather on the school's roof should
they make it to graduation day. There, they find the Main Character
lying in Aigis' lap, smiling at the brief reunion with the other SEES
members before he goes into a deep sleep.
The AnswerAn additional chapter of the story is available through the game's expansion
Persona 3 FES.
The events in The Answer take place on March 31, shortly after the end
of the original game; and with the end of school, the SEES dorm is to
be closed down. However, they find that while midnight has passed, the
rest of the world still believes it to be March 31. Resigned to
determine the reason later, the group departs to bed, but they are
awakened when Metis
appears in the dorm and attacks Aigis. Aigis fights back, her Persona
becoming that of Orpheus, the Main Character's original Persona. Aigis
is able to subdue Metis, and SEES learns that she is trying to end the
time skip by killing all the SEES members except for Aigis, who she
claims is her sister. Metis reveals that below the dorm is the Abyss of
Time, in which exist doors that lead to the past. SEES work their way
through the Abyss, reaching the doors, and ultimately obtain the means
to escape to either the present or the past just before the battle with
Nyx. After some internal strife as to which option to choose, they
discover a means to bring themselves to the moment Nyx was sealed, so
that they could learn why the Main Character fell into a coma and died.
They confront Metis on this, and she reveals that the seal created
by the Main Character was not to seal Nyx from humanity, but to prevent
humanity from calling out to Nyx. However, due to the buildup over
humanity's history, the wishes of humans that want to end their life
has manifested in the being Erebus,
who has been able to break through the seal, thus causing the time
skip. SEES is able to fight and defeat Erebus, and return to the
outside world. They learn that Metis is actually Aigis' desire to be
human, and with the threat over, the two fuse together, rendering Aigis
into a brief unconscious state as had occurred to the Main Character.
However, she shortly recovers, and with the rest of SEES, leave the
dorm one last time as they begin to go on with their normal lives.
P4Prior to the start of the school year, the Protagonist moves to the
rural town of Inaba, moving in with Dojima and Nanako, and quickly
gaining friends at the high school. Over the course of foggy nights,
two murders are reported, apparently tied in with the infidelity of a
local celebrity. The Protagonist learns of the Midnight Channel and
discovers that it reveals the identity of those who are about to be
murdered. He reveals to his friends he has the ability to enter the
Midnight Channel. There they meet Teddie, who explains that the victims
had been pushed into the Midnight Channel, and that when the fog in the
television world dissipates, they are met by shadows of themselves and
killed. The Protagonist and his friends realize that the murderer is
using this to his advantage, and are forced to save a classmate before
a foggy day when he/she falls into the same predicament. After helping
his friends face their own shadows and gain the ability to summon a
Persona and to enter the Midnight Channel themselves, they form an
investigation squad to learn the identity of the murderer.
The group is able to rescue several others that are forced into the
Midnight Channel through their investigations, with some of the
characters returning the favor by helping with the squad's
investigation. It is eventually revealed that Dojima's partner in the
force, Tohru Adachi, is the one responsible for the abductions, but
himself doing it for the goddess Izanami
.
Izanami wishes to show humans their true desires, bringing them all
into the Midnight Channel as Shadows, and covering the rest of the real
world in fog. The Protagonist, with the combined help of the
investigation squad and the Social Links that he has built up, is able
to defeat Izanami after transforming Izanagi into Izanagi-no-okami and
defeating the goddess with a single blow.
Persona 4 starts on April 11, 2011, which places the events of the
game at about twelve months after the end of Persona 3 FES, which ended
April 1, 2010.