Much of the second season premiere is about getting reoriented in this world, establishing who these characters are and where they stand. After flashing back to a young Kublai Khan taking lessons from his grandfather, we see Kublai at home in his role, attending to trade issues while also preparing for his son's wedding. Jingim is set to marry the Blue Princess, the former love interest of Marco Polo, securing more heirs to the throne.

It isn't long before the day of celebrations are spoiled, though. Kublai's bastard child Byamba shows up with a message from Kaidu, Kublai's cousin. Kaidu is still angry about not being handed the lead during the sack of Xiangyang, and he's prepared a form of retaliation. He's going to challenge the Kublai's rule as Khan in an attempt to secure the position for himself. Kublai does not accept such a ridiculous claim, but that's not the news Byamba brings back to Kaidu. There's a confrontation on the horizon this season, and it's taking place within filial boundaries.

Marco Polo and Mei Lin are traveling through the jungle with the boy emperor in their care. They're delivering the boy to Kublai, as Marco has been instructed, but their travel isn't easy. The boy's protector, who's known only as The Handmaiden, is still chasing after them, somehow able to keep up despite traveling on foot.

Meanwhile, Kaidu is doing everything he can to secure support for his claim to Kublai's throne. While on the one hand it's not a difficult sell because many believe Kublai stole the election long ago, there are also those who see going against Kublai as a dangerous act. Back in the new capital of Cambulac, Kublai is taking advice from his wife. She says that he needs to accept the challenge to his throne because Kaidu is operating within the law, and any other approach would suggest weakness or deceit.

Next, Marco and Mei Lin return with the boy emperor. The return sparks all kinds of intriguing relationships and power struggles. There's Kublai asserting his power over Mei Lin, even as Marco asks for leniency. There's Marco being "introduced" to the Blue Princess by Jingim and the awkwardness that follows from them being former secret romantic partners. There's also the issue of what to do with the boy emperor. While Jingim and Marco suggest letting the boy fade from the public's memory by stashing him in a safe place, Ahmad suggests killing him and parading his head through the streets to send a message. This is the same man who's working with Mei Lin to overthrow Kublai, even telling her that she could see her daughter in exchange for bringing the boy emperor to the capital.

The Blue Princess has a miscarriage, but Jingim is forgiving and understanding. Kaidu has his meeting with Nayan, who's preaching Christianity to the Mongolian masses, but they can't come to an agreement for him to back Kaidu's claim to the throne. Marco also tells Kublai of the many people in south China killing themselves, as they see the Mongolian presence not as liberation but as occupation.

As the boy emperor hangs from the capital, and the Handmaiden takes the sight in, Kublai awakes from another nightmare, his wife still lambasting him for his decision to kill a child. Marco isn't too happy with him either, and with both in crisis, Kublai takes his Venetian friend on a hike in order to decide what to do about Kaidu's claim to the throne.

The Handmaiden confronts Mei Lin - they both agree they have a common enemy. Meanwhile, the mounting pressure on the Blue Princess to produce an heir before Kaidu's claim comes to pass leads the Empress to force a stable boy with similar features to Jingim to impregnate the Blue Princess while the Empress holds her down. The Blue Princess tries to object that the resulting infant would not contain full royal blood to which the Empress responds, "actually, the baby will have no royal blood."

While this is happening, Jingim goes to Karakorum to help persuade people to side with his father. That means taking down a large warrior in a wrestling match and earning some respect, though that doesn't stop Kaidu's two children from attacking them on their way home. Furthermore, Kaidu makes a bold decision and insists that his daughter Khutulun, rather than his son, will be the next heir.

Nayan is in Northern Israel, along with Marco's father, to talk about Kublai. The discussion is rather simple. The Pope sees Kublai's rule as a threat, in part because since he's accepting of so many religions. The Pope vows to confront his forces should they move West. Nayan is less enthused about this idea, but when he proves his religious value to the Pope and the two agree to work together, he's swayed. He washes away his sins and prepares for battle.

Meanwhile, the hunt is on for Jingim and Ahmad. Kaidu is pissed at his son because of his actions, which have brought Kublai to his doorstep. Together they all go out to search for the Khan's missing sons. Along the way, Kaidu and Kublai connect with memories of their childhood but also remain divided on the prospects of the Mongol empire. Things get particularly heated when the insults start flying and Kaidu pulls his sword on Kublai. Ultimately, nothing comes of the moment as Jingim and Ahmad are found.

The other dangling plot thread is that of the Blue Princess and her potential pregnancy. Here she finds out that the stable boy who impregnated her has been killed, and when she goes to see the body for herself, she stumbles upon his wife and spends the day with her and her baby. It almost seems as if she'll abandon her position, especially if Jingim isn't found.

Five rebels execute five different attacks and kill 300 Mongolians, as Ahmad informs the Khan. Kublai states that while he'll still travel to Xanadu to challenge Kaidu, he gives Ahmad control of his forces to strike back.

Meanwhile, Khutulun makes it clear to Kaidu that she's not happy about being the heir because it would mean sacrificing her own goals. Byamba, who she's now separated from, is demoted to foot soldier by Ahmad, who's still working on his own plans to dethrone Kublai.

Ahmad gains even more control when a guard tells him about the Empress leading a stableboy into Princess Kokachin's chambers. The situation is about to get even more complicated because the real Princess Kokachin shows up, apparently not dead like we all believed, and wants her life back. At the same time, Marco continues to grow suspicious of Ahmad, especially as he decides to send nearly 60,000 troops to battle the uprising and only 7,000 with Kublai to Xanadu.

"Lullaby" also spends a bit of time filling in Ahmad's backstory. He was once simply a tax collector for the Khan, wanting to travel and learn about the people in Kublai's empire. He unknowingly has sex with his mother, a prostitute. When he realizes this, he kills her. This explains why he is secretly against Kublai.

First, as the episode opens, we see Kaidu and his mother secretly finding their way to Cambulac. They arrive in the middle of the night shrouded in hoods. The purpose of their meeting in the capital is to discuss the overthrow of the Khan with Ahmad. The Khan's Vice Regent has made it clear that he wants Kublai gone, and he sees Kaidu as his own tool. In addition to Kaidu, he invites Nayan for the meeting, securing both of their opposition to Kublai. The offer of Mei Lin's daughter to the sinful Nayan helps to sway him.

Meanwhile, Kublai is in Xanadu petitioning for votes and arguing for his vision of empirical expansion, complete with fireworks, to the people there. There are harbingers of death all around, though. Horses that were gifted to Kublai are attacked, found with their eyes carved out. Marco and Jingim believe it's the work of Kaidu, but Kublai doesn't seem worried. Eventually, after a night of passion with an exotic dancer who's traveled the world, the Blue Princess visits Marco and the mystery of the horses is solved.

Under pressure from her pregnancy and guilt over her child and the dead stableboy, the impostor Blue Princess suffers a nervous breakdown; the real Blue Princess that had been demanding her life back was nothing more than her hallucination and it was the impostor Kokachin that had been gouging out the eyes of the Khan's horses. Marco points out to her the blood all over her hands.

We see that Hundred Eyes and the Handmaiden, who he refers to as Lotus, were once friends and lovers. When the Mongolians attacked them, Hundred Eyes thought he saw Lotus die at the hands of an archer.

The second attack is undertaken by Khutulun and Orus on the order of Kaidu. He's conducting murderous raids under the banner of Kublai, having his children and warriors wear masks to conceal their identities. Essentially he's framing Kublai in the hopes of drumming up support for his ascension to the throne.

Meanwhile, the Blue Princess's visions threaten to reveal the true nature of the baby. Jingim is upset by his wife's condition. However, after Kublai finds out about Kaidu's attacks under his own banner, Jingim is ordered to ride East to engage in their own attacks. That's all part of Ahmad's grand scheme, though: send Jingim east to die while Nayan and Kaidu amass troops in the west.

There's a twist that Ahmad doesn't expect: Mei Lin turns on him after he fails to deliver on his promise for her to see her daughter. That sends her to Marco, who gives her time with her daughter, and in return she tells him everything. Marco goes to the Khan and asks for his permission to head west even though he can't reveal why. He's asking for trust, and Kublai gives it.

First, Ahmad lies to Kublai about Jingim's attacks in the East - Marco and Jingim are actually headed West - and when Mei Lin goes missing, Kublai questions his Vice Regent's connection to her.

At the same time, Niccolò goes missing from Nayan's camp near the Twin Rivers, captured by Marco and Byamba. They spend the entirety of "Whitehorse" hiding in the woods, Marco questioning his father about where they will attack the Khan, and his father essentially calling him a traitor to his Christian people. For a while it looks like Marco has no choice but to kill his father, but a last-minute attack leaves the elder Polo's fate hanging in the balance.

As for Mei Lin, she's escaped her entrapment with Ahmad, daughter in tow, and when Mongols attack her on the road, Lotus comes to her aid. That forces Mei Lin to accept that the Mongols will keep coming after her and her daughter until she ends this feud, so she leaves her daughter in the care of Lotus, the same woman who couldn't protect the boy emperor.

"Heirs" begins with the Khan's force's attack on Nayan and Kaidu's camp. Borrowing an unconventional battle tactic from his grandfather Genghis, the Khan lights all of his white horses on fire and sends them charging through the enemy camp. This ingnites their black powder, which rips through the stronghold.

Moments before the Khan's cavalry charge into the camp, Niccolò orders Kaidu to escape to Karakorum in order to preserve their plan of dethroning the Khan at the Kurultai. After some hesitance, Kaidu relents. During the melee, Byamba and Marco fight side by side. Hundred Eyes encounters a knight in chain mail, whom he dispatches with a well-placed jab to the neck. Khutulun and Orus face Jingim but she leaves to save Byamba from a rebel. This allows Jingim to overpower Orus and bash his skull in with a rock. Marco intervenes and saves his father from the Khan's men, allowing him to escape, which the Khan sees from a distance and once again sows doubt about Marco's loyalty in the Khan's mind.

At Karakorum, Kublai and Kaidu await the outcome of the Kurultai. Ahmad sits on the Khan's throne in Cambulac. The episode also foreshadows the plot of the show's third season with the arrival of a new adversary: Prester John.

Two storylines make up "The Fellowship." The first involves the cases both Kaidu and the Khan give at the Kurultai as to why they should earn the Mongolian noblemen's votes in order to be selected as the Khan of Khans. It looks as if the vote is all but settled, with the people siding with Kublai and protesting Kaidu's aggressive tactics. The Kurultai doesn't go down without a hitch. Ahmad, backed into a corner by the presence of Jingim, Byamba, and Hundred Eyes, sends word to Kaidu revealing the truth about Jingim's son and Kublai's heir.

Kaidu uses that knowledge to blackmail the Khan and the Empress, but they're more determined than Kaidu gives them credit for. First, the Empress helps the Blue Princess drown herself, and Kublai attempts to poison Kaidu, hoping to stop the potential leak of the information. Kaidu gets the upper hand, though, and is moments away from killing Kublai when Marco saves him. He has come back from his banishment to inform the Khan about Prester John's approaching Christian army. He kills Kaidu, thereby proving his loyalty to Kublai in the process.

Back at Cambulac, Jingim, Hundred Eyes, and Byamba expertly pull off a raid that sees them take back control of the capital as Ahmad runs and hides. Unfortunately for him, Mei Lin is waiting for him in his room. She kills him and, in return, Jingim allows her to leave the capital freely, with Hundred Eyes offering to escort her back to her daughter.