As the main progatonist of Shin Megami Tensei IV, Flynn is the player character; all the decisions you make influence how the game unfolds. He is first introduced having a dream where he meets Walter and Jonathan, much like how SMT I starts. He is then introduced with his friend Issachar, where they head to Mikado Castle to attempt the Gauntlet Rite; He succeeds while Issachar does not.
After a series of training exercises, his home town is set ablaze. He, Walter, Jonathan and Isabeau all acompany him to help his villagers, only to find it was Issachar's doing, whom is possessed by a demon. You are given the choice to spare or kill him during the fight, receiving both criticism/praise from either Walter or Jonathan. Attempting to confront the Black Samurai about this, he is stopped by a horde of Lilims.
After the rescue mission of Kiccigiorgi, Flynn and company are sent to go after the Black Samurai. This leads them deeper into Naraku, which connects to Tokyo. It is there they learn of her wherabouts in Ikebukuro. Once captured, they take the Black Samurai back to the Eastern Kingdom of Mikado, where she will be publicly executed.
The next day, Sister Gabby calls upon all four Samurai who went to Tokyo to do two tasks. The first is to rescue 3 men who are important to Mikado. During this mission, the archfiend guarding one of them mentions if they are rescued, it will be the end of Tokyo. Once rescued, You return to Sister Gabby for your second Task: Killing the Black Samurai. She informs you that she has been resurrected.
Once back in Tokyo, you bump into the leader of the Ashura-Kai: Tayama. He has a samurai hostage and forces you to do some things for him, the last being to kill someone called Yuriko in the Ring of Gaea in Ginza. Once arrived, you take a test to join the Ring of Gaea to meet Yuriko in person, however, you are found out and are dropped in a hole into the Passage of Ethics (This is important to your alignment, so be wary of your choices). After you pass through, Yuriko meets with you and it turns out shes the Black Samurai, but in turn is actually Lilith. Walter Stops the group from trying to kill her when she states that you should see what True Evil is. While not enthusiastic about it, the group returns to Roppongi and heads to midtown, where there is a reverse Roppongi underground. Here, you find that Tayama has a human farm and plucks out Nuerotransmitters from the brains of people to create red pills, a substitute food for demons. Having seen this, you are knocked out cold by a demon Tayama has and is brought back into his office. He attempts to explain his actions and you are told once more to kill Yuriko/Lilith.
You are shortly stopped by Hugo of Mikado to return and meet Gabby at Shene Duque, a giant cocoon. There you are greeted by the three men you had rescued, who were Uriel, Michael and Raphael. Gabby then reveals herself to be Gabriel and tells you that you are to kill the Black Samurai once more. There, Walter and Jonathan split paths and you are forced to choose who to side with. Isabeau, not content with the situation, decides to think about all that's happened and splits from you as well. Depending on who you choose to go with will affect your alignment as well as what story elements occur here.
Should you Choose to go with Jonathan, you go to Tsukiji Hongwanji to kill Lillith, but are warned that something is up at the Yamato Reactor. Once you arrive in Shibuya and head to Camp Ichigaya, where the reactor is, you end up bumping into Walter who has killed Tayama and activated the reactor, sucking the three of you in.
If you go with Walter, you meet up with Lillith to receive the mission of activating the reactor itself. While on the way there, you are stopped by The National Guard divinities, amongst them is Koga Saburo once more. After defeating them and reaching the reactor in Camp Ichigaya, Tayama warns about turning it on and yells at the protagonist. After pressing it, Tayama is sucked in by the reactor to the demons, then you and Walter are sucked in.
Either way, you arrive into a world of White, greeted by 4 people known as the White, who tell you about what might happen should you make an important decision regarding the state of the world. They then proceed to show you what might happen if you decide to preserve the Status Quo. Depending on who you went with to Camp Ichigaya, different dialogue is mentioned when you wake up in Kasumigaseki with Walter and Jonathan, who were arguing. They go outside only to see ground zero. The tokyo you were sent to is one where God had decided to destroy the world because it did not follow his will. You find a group of people still living in shelters, wearing gas masks since the air is polluted with poison. Their leader, Akira, tells the group that they need Pluto the Tormenter defeated, upon which he will give you the remote to the Yamato Reactor.
Once you complete this tokyo, you get sent to another tokyo, an Infernal one. One of which the citizens have decided to fuse with demons and fight for territories. You bump into another Akira, one who is half-demon, and he wants you to help him defeat Kenji, the current King of Tokyo. He states that they must stop by Shinjuku first to expand their territory.
Both Akiras tell the three of you something unexpected. The Akira of Ground Zero states that he's ok with demons coming from the Expanse, and will take control if necessary. The Akira of the Infernal Tokyo wants to bring back equality in the world, seeing that they need it once again. Taking this into consideration, the White bring you back and ask you an ultimatum.
They ask if you want to bring the world back to naught seeing as there is no escape from God's will. Should you accept, they ask you to destroy the Yamato Reactor, which will suck up the universe.
Should you decline this and your alignment is leaning LAW (and chose to preserve the status quo), you get sent into the monochrome forest, where Jonathan greets you as well as Gabriel, who tells you to defeat the White to leave. Once that is done, you are brought back to Shene Duque, where the 4 heralds mention that the gate to the expanse has opened and Lucifer has been resurrected. They ask one of you to be a martyr and become God's Chariot: Merkabah. Jonathan, after consideration, will do it, even if you choose to do so.
After said transformation, Merkabah goes with you to go and destroy tokyo, seeing that the influence would be too great for the Kingdom of Mikado. Once you arrive at Camp Ichigaya, you are stopped by Isabeau, who wishes to stop you seeing that the action you are taking amounts to genocide. You end up killing her and head of to Lucifer's Castle. After defeating them, Merkabah states that both of you have brushed with the unclean ones and pushes the button to the reactor, releasing the black hole and killing both of you along with tokyo.
A while later, Jonathan talks as a backdrop to mention how peace lasted forever in Mikado and you were remembered as a sacrifice.
Should your actions and decision leave you in the middle, you are sent to the monochrome forest, alone. There, Steven greets you again and tells you that the spirit of tokyo needs to be restored. Burroughs also seems to have prior knowledge on who Steven is. Upon defeating the white, Steven tells you that a way to return things to normality would be to revive Masakado, and he sends you back to reality. You wake up at the Counter Demon Forces' base and greeted by Isabeau, who was looking for help.