In the deserts of the Khyber Pass, Ghiaz Beg's caravan is attacked by ruthless bandits while his wife Asmat is in agony giving birth to his third child and first daughter. Thanks to the birth of this innocent newborn, the bandit spares his family considering it's a girl & they're doomed any way. Ghiaz's family continues on along until they meet a nobleman who takes them all to meet Akbar.

Jagat Gosini, the Rajput princess betrothed to Salim, is on her way to Lahore. Salim visits Man Bai, his wife & sister to Man Singh - one of Akbar's military commanders. Man Bai expresses her concern and discontent to Salim's second marriage who reassures her that this is a political alliance and that she will always have a special place in his life.

Ghiaz's family is invited to Salim's wedding, but Nissa is barred because of her altercation with the Pandit. She emotionally manipulates her angry parents and is allowed to attend the wedding with the family. At the wedding, Nissa finally sees the palace and, due to her excitement, is slapped by Hoshiyaar. Ruqaiyya Begum notices her and asks for her to be sent to the zenana the next day.

Nissa readies herself to visit the palace. Upon arriving there her excitement is palpable. But on her very first day she sees Ruqaiyya lock horns with Princess Jagat and she gets got in the crossfire. Princess Jagat catches Nissa laughing involuntarily at her, and thinks it impertinent.

Akbar's birthday preparations take place with great fanfare. Unspoken kitchen politics begin, as Jagat and Ruqaiyya both start preparing meals for the Emperor. It becomes a competition of sorts, to see who will impress the Emperor the most.

Prince Salim organizes a qawwali on Akbar's birthday. On seeing his father's closeness with his youngest brother, Daniyal, and fearing the loss of the throne to him, Salim decides to do the unthinkable. Akbar suffers an attack as a result of food poisoning. Khan-I-Khanan and Fazl decide to investigate and get hold of all the cooks and tasters to find the culprit behind the poisoning.

Mahabat wants to get rid of Abul Fazl to ensure the safety of Prince Salim. The prince diverts his focus to the impending war campaign while the king recuperates. Abul Fazl reminds Mahabat again that with Akbar springing back to life, he is getting closer to proving to everyone that it was Prince Salim who poisoned his father. Young Nissa meanwhile, is enamored by the Mughal way of life.

Nissa and her family return to Lahore. Now 16, the confident and beautiful Nissa turns up at the zenana, much to Ruqaiyya's joy. She also meets Khurram, now 6, and the two take to each other with ease. Pleased, Ruqaiyya asks Nissa to look out for Khurram, an arrangement that she accepts wholeheartedly. Salim's troops return after losing the extremely arduous Rajputana campaign.

Nissa receives a note from Salim saying he wants to see her but Nissa plays hard to get. Jagat Gosini gets wind of this budding romance but ignores it thinking it as just another affair for Salim that fizzle out in due time. Salim comes to meet Nissa while she is tending to little Khurram. The two sneak away and indulge in some harmless flirtation. The sparks of a tempestuous romance are visible.

Koka and Mahabat warn Salim that Daniyaal's trying to win favor in the court and the zenana. Salim needs to be wary of him, but Salim seems to be lost elsewhere. During another romantic rendezvous, Nissa gives Salim some valuable advice. Salim tells Akbar he wants the campaign in Rajasthan & not the one in Deccan. Abul Fazl & Daniyaal can't believe the Deccan campaign has landed in their laps.

Salim gets Nissa a beautiful bracelet, meeting her at Meena Bazaar to sneak away. Soon, everyone in the zenana is talking about their romance. Mahabat and Koka find out Nissa advised Salim to let Daniyaal have the Deccan campaign and are startled to learn Salim is taking political and strategic advice from a woman. Mahabat sends Hoshiyaar Khan to Jagat Gosini and requests a secret meeting with her

Salim goes to spend time with Daniyaal but is greeted with hostility. Mahabat secretly meets Jagat and tells her she needs to be careful of the new woman in Salim's life, for she may be a threat to everyone concerned. Jagat ignores Mahabat's warning and claims she won't feel threatened by a commoner such as Mehrunissa. But in reality, Jagat feels she must start taking precautionary measures.

Akbar rewards Ali Quli handsomely for saving Khan-i-Khanan's life. Hoshiyaar Khan spreads rumours about Nissa & Salim. Jagat tells Man Bai they should try to end Salim's affair with Nissa, but Man Bai accepts that Salim will take other wives & isn't interested in the plan. Nissa hears the rumours about her & meets Salim one last time to end the affair, but Salim says he wishes to marry her.

Nissa informs Asmat of Salim's marriage proposal and that he will soon come over to discuss it with the family. Salim, wanting to be brotherly, asks Daniyaal to let go of his burdens and focus on his wedding. He also gives marital advice to Daniyaal while also hinting at his own marriage with Nissa. Meanwhile the powerful and great Akbar, is shattered knowing that his own son tried to poison him

Salim finds out Nissa's is to be married with Ali Quli, and rushes to meet Akbar but is denied. Salim promises Nissa to seek Akbar's approval on their wedding. Abul Hasan is apprehensive and asks Nissa to act smartly. Mahmud overhears the conversation and the information is relayed to Akbar. Salim unsuccessfully tries to meet Akbar again. Nissa and Ali Quli are engaged, much to her reluctance.

Nissa & Abul Hasan ride to the palace to meet the prince. Salim meets Akbar and pleads for Nissa but realizes it is Akbar's imposter. Nissa is hopeful things will soon be alright. Abul Fazl warns Salim that Nissa will be beheaded if Salim does not put the affair behind him. Nissa waits for Salim but Koka tells her Salim has chosen the imperial throne over her. Heartbroken, Nissa marries Ali Quli

Nissa's upset about being married off to Ali Quli and is unforgiving towards her family. She is surprised by the arrival of Yasmin and Nawaz from the royal palace. Ali Quli is angry on finding her telescope, a gift from Salim, but Nissa tells him she is married to him and he shouldn't be worried. She asks Yasmin to get rid of the telescope and tells Abul Hasan she is dispassionate about Salim.

Mahmud is growing in prominence at the royal palace and is extremely hurtful towards Nissa. She reminds Mahmud that she still knows everything he is up to, hinting at his affair with Hoshiyaar. She expresses her pain to Ruqaiyya as well. Akbar and Nissa share an awkward moment when Khurram introduces her to his grandfather. Nissa is dealt a blow from fate when she has an untimely miscarriage.

Nissa, unable to deal with the pain, avoids meeting Asmat and Mahmud, and tries to find out more about Nawaz. Yasmin tries to help and suggests Nissa meet a hakim. Nissa forces the hakim to give her some poison. On a shikaar together, Ali Quli mentions to Salim about Nissa's miscarriage, cursing her for it. As Ali Quli walks away, an offended Salim lets go of a bullet in his direction.

Ali Quli arrives home with a scroll from Salim. Nissa, while planning to consume poison, comes across Salim's scroll and on reading it, breaks down. In sheer desperation, Salim tells Akbar that his campaign has been the best of the three and Akbar admits it, rather haughtily. Salim notices that Akbar is besotted with Nadira and this is reaffirmed when he sees Nadira in his father's tent.

Salim meets Nadira under the pretext of developing a friendship with her. Koka tries to convince Salim to stop playing with Nadira's feelings, but Salim is vengeful and won't stop till his mission is accomplished. When Salim compares Nadira to Pasha Begum, Akbar is surprised, promises Salim to find him a lovely wife soon. Salim meets Nadira & gets her to promise him that she'll meet him again.

When Nadira informs Salim that she could be in love with him, he is stunned. He didn't think his attempts at getting back at Akbar would land him in such a situation. Nissa tells her father that she would like to give her husband a chance for things to fall into place. When Nadira steps out of Salim's tent, she is spotted by Akbar's hakim, who informs the Emperor of the same.

Akbar calls off the Rajputana campaign. Koka tells Salim that his imbecility might have rendered Nadira dead. Back in the palace, Jagat provokes Ruqaiyya Begum by mentioning Nadira. Ruqaiyya visits Nissa, asks her to get her act together. Nissa decides that Yasmin will stay and that she will make her suffer. Mahabat and Koka suggest they attack Agra fort. Salim readily agrees.

Defying the heat, Salim and his army march towards Agra fort. Daniyal smuggles alcohol in a musket and the gunpowder laden musket, poisons him to death. News of his son's death reaches Akbar. The grieving Akbar is informed about Salim's decision to attack the fort. At Daniyal's burial, Akbar wonders about the future of the Mughal Empire.

Salim receives news of Daniyal's death while he tries to find ways to get into Agra fort. Meanwhile, Nissa suffers another miscarriage. On learning from Ruqaiyya that she is heading to Salim's camp to stop him from revolting against his father, Nissa gives her the bracelet and asks Pasha Begum to pass it on to Salim.