Magnus and the Dark Lord is the second chapter in Kid Icarus: Uprising for the Nintendo 3DS. It goes further in-depth in the storyline, expanding on the war going on between the nations. This chapter also introduces a few new areas to the game, including the Zodiac Chamber and a luxury called the Hot Spring. Two new characters are met - Magnus, a bounty hunter that is known as the strongest of the humans, and Gaol, a Dark Lord in Medusa's army.
 Air Battle
This chapter begins with Pit flying through a dark, stormy sky. Lightning sent from the Underworld Army is able to injure the angel, eventually finishing him off, if it isn't evaded. However, it is easy to dodge, as light appears before the lightning hits a specific area. Eventually, Palutena sends Pit into a large tornado in order to give chase to the Underworld Army, but Pit is halted by Gyrazers in the process. Luckily, he makes it out and enters a ridge in the ground, a canyon, where he must fight off numerous Underworld enemies. Later on, Pit reaches a dark cave underground, and he and Palutena remark that the "Underworld baddies" seem to enjoy it. They are then ambushed by Gyrazers. Porcuspines and many other various enemies. Once Pit re-enters the outside world, he is quickly chased down by a Belunka spitting out enemies such as Monoeyes and Miks. The angel is able to stop the beasts, and quickly flies away.
Palutena then leads Pit with the Power of Flight up over a giant wall that stands in his way of reaching Gaol's Castle. Here, they are attacked by many different enemies that Pit easily defeats, and then he glides over a giant wasteland with the warring humans below. He exclaims that the humans need their help, but Palutena can't keep the Power of Flight going for more than five minutes, so she takes him immediately to Gaol's Castle, where he lands and begins to pursue the Dark Lord himself.
 Land Battle
When Pit lands, he is seen on a terrace outside of Gaol's Castle with various food items surrounding him to recover health. The first enemy Pit encounters after opening a door through the use of the first switch in the game is a Monoeye. However, he soon meets with Skuttlers and Skuttler Cannoneers. After he defeats them, he gains access to a Treasure Chest that is holding a weapon of some sort.
When Pit goes up the stairs, he is met by a door that is locked. To unlock it, he must defeat a Boogity on the right side and flip the switch behind it and flip the switch on the left side of the room. When he does, a Ganewmede appears in front of the door, which is easily defeated through the use of melee attacks.
As Pit advances through the castle, he will eventually run across Magnus, a human mercenary working to make some money with the defeat of Dark Lord Gaol. He is an extremely powerful human, as exclaimed by Palutena, and quickly begins to assist Pit with the ambush of monsters in the room. He later proves to be very skilled with traveling, as he can tell when there is a Mimicutie around, telling Pit that he knows its a decoy. After they meet and fight together for a little while, they travel forward and enter Gaol's throne room.
 Zodiac Chamber
In the hallway before finding Magnus and the monster ambush, there is a wall that appears to be transparent. If Pit decides to pass through it, he will find the very first Zodiac Chamber in the game. This one contains the Sagittarius Bow.
 Boss Battle
When Pit and Magnus first enter the chamber of Gaol, the battle begins. Gaol and Magnus begin to have a conversation, and it's made obvious to Pit that they used to know each other from somewhere. Gaol uses things such as suction vortexes to stop Pit and pull him in just before attacking him with a dark attack. He will also summon Skuttlers by his side, to which Magnus asks if these are the "new recruits", confirming Palutena's thought that they used to be in a mercenary group together.
After Pit and Magnus defeat Gaol, it is revealed that she is actually a young woman with blonde hair, and Magnus kneels next to her body and apologises. Pit is sorry for 'killing' a human, but is told by Palutena how she looks to be still hanging-on, before he is whisked away back to Skyworld.
This chapter contains one of the first references to Kid Icarus' brother series, Metroid, in which Gaol losing her amour and turning out to be a young woman is reminescent of the first Metroid game, in which it turns out the player-character, which is assumed to be an android or a muscular man in a suit of armour, turns out to be a blonde-haired woman after her armour disappears.