Somewhere 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 new born, the bandit spares his family considering it's a girl child and they're doomed any way. Ghiaz's family continues on along the unforgiving path until they meet nobleman Masood, who in a twist of fate, rescues the Beg family and takes them all to meet the emperor of Hindustan Akbar. 12 years later, Ghiaz is a part of Akbar's court while his daughter Mehrunissa (Nisa), grows up to be a bright and precocious child always brawling with her older brothers Mahmud and Abul.
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. Their son Khusrau has a reputation for being slightly eccentric and dangerous. 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 & his family are invited to Salim's wedding with Jagat, in which Nisa is barred because of her altercation with the Pandit hired to teach her. Meanwhile Nisa's sulking & emotional manipulation melts the will of her angry parents and she is allowed to attend the wedding with the family. At the wedding, Nisa finally sees the palace and, due to her excitement, is slapped by Hoshiyaar. This also allows her to be noticed by Ruqaiyya Begum, who asks for her to be sent to the zenana the next day.
Nisa 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 Nisa 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 the occasion of 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 try to get to the root of the poisoning. Mahabat and Koka assure Prince Salim that their tracks have been covered but when they learn about Khan-I-Khanan's order for all the hakims to be brought to the palace, Mahabat hires an assassin to get their hakim killed. The assassin manages to kill all the captive hakims. Fazl tells Prince Salim that he is aware of his master plan to poison his father and that he will leave no stone unturned to find out the truth. When Akbar tells the young Prince that the throne is his for the taking, he is ashamed of his deed.
Mahabat wants to get rid of Abul Fazl to ensure the safety of Prince Salim. The prince on the other hand, diverts his focus on the impending war campaign while the king recuperates. Abul Fazl reminds Mahabat again that with Jahanpanah Akbar springing back to life, he is getting closer to proving to everyone that it was Prince Salim who poisoned his father. Young Nisa meanwhile, is enamored by the Mughal way of life and under Ruqayya's watchful eye, learns many life lessons too. Her mother insists that the young, loquacious girl be married though. Ruqayya reminds Man Bai that as Salim's first wife, she will have to constantly make him realize her worth but her efforts hit a roadblock when she discovers that Jagat Gosaini is pregnant. True to her nature, Jagat Gosaini doesn't shy away from letting Man Bai and Ruqayya know that she will soon be mother to the possible future ruler of Hindustan.
Nisa and her family return to Lahore. Now sixteen, the confident and beautiful Nisa turns up at the Zenana, much to Ruqayya's joy. She also meets Khurram, now six, and the two take to each other with ease. Pleased, Ruqayya asks Nisa to look out for Khurram, an arrangement that she accepts wholeheartedly. Salim's troops return after losing the extremely arduous Rajputana campaign. The dejected Prince refuses to meet his father. Abul Fazl uses Salim's absence to his benefit by welcoming young Prince Daniyal to court, who has just arrived at Lahore after tasting success at Kashmir. Mahabat and Koka remind Salim that he has a contender in Daniyal and must tread carefully if the throne must be his. Similarly, Abul Fazl ensures that Daniyal begins to understand that Salim hates him and thinks of him as competition. Seeds of doubt and thoughts of immense hate begin to take root in both the brothers' minds and hearts.
Nisa receives a note from Salim saying he wants to see her but Nisa 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 Nisa while she is tending to little Khurram. The two sneak away and indulge in some harmless flirtation. The first sparks of a tempestuous romance are visible.
Koka and Mahabat warn Salim that Daniyaal is trying to win favor in the court as well as the zenana and Salim needs to be wary of him but Salim seems to be lost in another world. He and Nisa have another romantic rendezvous. During this meeting, Nisa gives Salim some very valuable advice. Salim tells Akbar that he wants the campaign in Rajasthan and not the one in Deccan. Abul Fazl and Daniyaal cannot believe their luck as the prestigious Deccan campaign has landed in their laps.
Salim sends Nisa a beautiful bracelet and later meets Nisa at the Meena Bazaar to sneak her away. This romance begins making the rounds of the rumor mill and it isn't long before everyone in the Zenana is talking about it. Mahabat and Koka find out that it was Nisa who had advised Salim to let Daniyaal have the Deccan campaign and they are livid. It becomes apparent to them that Salim's attraction towards Nisa is not merely physical. They are flabbergasted to learn that Salim is taking political and strategic advice from a woman. Both decide to take action. Mahabat sends Hoshiyaar Khan to Jagat Gosini and requests a secret meeting with her.
Salim goes to spend time with Daniyaal but he is greeted with hostility from his brother. Meanwhile, Mahabat meets Jagat in secret and tells her that she needs to be careful about the new woman in Salim's life for she may be a threat to everyone concerned. Jagat ignores Mahabat's warning and claims that she isn't one to be threatened by a commoner such as Mehrunissa but in reality, she feels she must start taking precautionary measures all the same.
Ali Quli is introduced to Akbar by Khan-i-Khanan in court. Akbar rewards him with a handsome mansab for saving Khan-i-Khanan's life. Hoshiyaar Khan, on Jagat's behest, spreads vicious rumours about Nisa and Salim. When Jagat meets Man Bai, she tells her that together they should try to end Salim's affair with Nisa. Man Bai has come to terms with the fact that her husband will take other wives. She is not interested in scheming against Nisa. Nisa gets wind of the rumours circulating about her and meets Salim one last time to end the affair as it is hurting her reputation. Salim reassures her he has every intention to marry her.
Nisa informs Asmat of Salim's marriage proposal and that he will soon come over to discuss the same with the family. Salim, in trying to remain brotherly with Daniyaal asks him to let go of all his burdens and focus on his wedding. He also gives marital advice to Daniyaal while also hinting at his own marriage with Nisa. Meanwhile the powerful and great Akbar, is shattered knowing that his own son tried to poison him.
Salim, on finding out that Nisa's marriage has been fixed with Ali Quli, rushes to meet Akbar but is denied entry. He confronts Abul Fazl, Koka and Mahabat in sheer desperation. At the other end, Nisa is upset with her parents for having accepted the proposal without much resistance. Nisa rushes to the palace to meet Salim and when they meet, Salim promises to seek Akbar's approval on the wedding, on the morning of Eid. Abul Hasan expresses his apprehensions about Salim's promise and asks Nisa to be smart about her decisions. Mahmud overhears the conversation and passes on the information to Hoshiyaar, who relays the same to Akbar. Salim tries to meet Akbar one more time but is forced to return unsuccessfully. Finally Ali Quli, accompanied by Khan-I-Khanan, comes to Nisa's house where Nisa and Ali Quli are engaged, much to her reluctance.
In an attempt to meet the prince, Nisa and Abul Hasan ride to the palace. Salim meets Akbar before the Jharoka darshan and pleads for his love only to realize that he is talking to Akbar's imposter. Nisa watches Salim and Akbar and is hopeful that things will soon be alright. Abul Fazl warns Salim that Akbar has ordered for Nisa to be beheaded if Salim does not put the infamous affair behind him. Nisa waits for Salim but meets Koka instead who tells her that Salim has chosen the imperial throne over her. Sad and crestfallen, Nisa gets married to Ali Quli.
Nisa, still upset about being married off to Ali Quli, is in an unforgiving mood towards her family. Nisa is surprised by the arrival of Yasmin and Nawaz, who they claim, have been sent from the royal palace. When Ali Quli threatens her on finding the telescope, a gift from Salim, Nisa tells him that he has nothing to worry about; she is married to him and will not give him any reason to complain. She asks Yasmin to get rid of the telescope immediately. She even tells Abul Hasan that she is dispassionate about Salim and his doings.
Mahmud, by virtue of his growing prominence at the royal palace, is extremely hurtful towards Nisa. Nisa, though distraught and powerless, reminds Mahmud that she still knows everything he is up to when she hints at his affair with Hoshiyaar. She expresses her pain to Ruqaiyya too who can sense that she's still hurting. Even Akbar and Nisa share an awkward moment when Khurram introduces her to his grandfather. Nisa is dealt a further blow from fate when she has an untimely miscarriage.
Nisa, unable to deal with the pain, avoids meeting Asmat and Mahmud, and tries to find out more about Nawaz. Yasmin tries to help Nisa bounce back to life and suggests that she meets a hakim. Nisa forces the hakim to give her some poison. On a shikhaar that Salim and Ali Quli set out on, Ali Quli mentions to Salim about Nisa's miscarriage, cursing her for it. Salim takes offence to it and as Ali Quli walks away, he lets go of a bullet in his direction.
Ali Quli arrives home with a scroll from Salim. Nisa, 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 wanting to develop a friendship with her. Koka tries to convince Salim to stop playing the fool with Nadira but in vain. Salim is revengeful and won't stop till his mission is accomplished. When Salim compares Nadira to Pasha Begum, Akbar is surprised; tells Salim that he will soon find him a lovely wife. In another attempt, Salim meets Nadira and gets her to promise him that she will meet him again.
When Nadira informs Salim that she could be in love with him, he is stunned. Not for a moment had he thought that his attempts at getting back at Akbar would land him in a situation like this. Nisa tells her father that maybe her husband deserves a chance and that if she gave him some time, things would 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 Nisa; asks her to get her act together. Nisa decides that Yasmin will stay and that she will make her suffer. Mahabat and Koka suggest they attack Agra fort. Salim readily agrees and makes an offer to his commanders.
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, Nisa suffers another miscarriage. On learning from Ruqaiyya that she is heading to Salim's camp to stop him from revolting against his father, Nisa gives her the bracelet and asks Pasha Begum to pass it on to Salim.
Nisa continues treating Yasmin badly. Ali Quli riles Nisa about not being able to give him a child. Nisa decides that Yasmin will have her child at Ali Qulis house. Meanwhile, Ruqaiyya tries everything in the book to stop Salim from revolting against Akbar. Salim contemplates the attack on the fort. As a last try at persuasion, Ruqaiyya gives Salim Nisas bracelet.
Mahabat and Koka celebrate Fazls death but their celebrations are brought to a halt when Salim decides to call off the attack on the fort. Koka and Mahabat plan on attacking the fort, anyway. Much to their dismay, Salim stops them at the forts entry and threatens to have them beheaded if they ever repeated the mistake again.
Nisa refuses to let Yasmin abort the child. Salim writes to Nisa and returns the bracelet. Akbar and Ruqaiyya talk about the possibilities of the future king, with Ruqaiyya telling Akbar that Salim is remorseful over things he has done in the past. Meanwhile, Yasmin delivers a baby boy. Nawaz suggests that Nisa keep the baby; Nisa refuses and warns Nawaz to not harm Yasmin in any manner. After a time lapse of four years, we see Abul Hasan giving Salim a lowdown on crucial matters in Lahore and Nisas pregnancy.
Nisa gives birth to Laadli. Ruqaiyya visits Laadli and asks Nisa to pray for Salims return. When Ali Quli discusses courtly matters with Nisa, she wonders how Khusrau will gain support at court and from the people. She writes to Salim. Akbar apologizes to Ruqaiyya for his indiscretion over Nadira. Murad dies but not before telling Akbar that Salim will return to Lahore. While on his way back, Salim receives news about Murads death and is shattered.
Khusrau challenges Salim to a kushti match. Jagat tells Salim that by accepting Khusrau's challenge, he has acknowledged the young prince. Salim says that if he hadn't accepted the proposal, he would be spoken about as a coward prince. Salim asks Nisa to meet him. Nisa tricks Ali Quli into believing that if she goes to the zenana more often, she will have information for him on the Khusrau front. Nisa meets Salim and they share a romantic moment. Nisa asks Yasmin if she was sent to her by Salim.
The people of the kingdom worry about Akbar's ill health. Painful rumors abound. People wonder who their next king will be. Ruqaiyya is irritated with people pouring in, 'concerned' about the king's ill health and pours her heart out to Nisa.
Akbar grants Salim the permission to do as he pleases with the enemy. Akbar crowns Salim the next Mughal emperor and pleads to know the truth about Fazl's death. Salim lies about his involvement and Akbar passes away peacefully. Salim is now Shehenshah-E-Hind Jehangir. Ruqaiyya leaves for the Dowager palace and Asmat urges Ghiaz Beg to speak to Jehangir for Mahmud and Ali Quli's acquittal. Jehangir meets Nisa and she asks him to be fair with Ali Quli and punish him in the same manner as he would the other prisoners.
Jagat asks Mahabat to ensure that Ali Quli isn't killed but is sent away. In return, Mahabat asks her to ensure that he's made the wazir-e-Azam. Jehangir punishes the dissidents and grudgingly sends Ali Quli and Nisa to Burdwan. When Ali Quli leaves for Burdwan with Nisa, she receives the new coin and is reminded of the time when she received a coin from Salim as a child.
Man Bai pleads with Jehangir to forgive Khusrau. Khusrau on the other hand, requests permission to visit Akbar's grave. Jehangir says he'll decide on both matters after his return from the shikhaar. Both Man Bai and Hoshiyaar, on bumping into Khusrau, ask him to be wary of doing anything that would anger Jehangir. Man Bai kills herself on hearing the news about her son's escape.
Jehangir learns about Khusrau's escape and advancement towards the Agra fort. On their arrival at Agra, Nisa informs Abul Hasan of Ali Quli's plan and her brother tells her about their father's strange behavior. Jehangir has a dream wherein Akbar tells him that his sons will give him insurmountable pain, foreshadowing the future. In spite of Koka and Mahabat's requests, Jehangir decides to fight his son. On hearing about his mother's death, Khusrau commands his unprepared army to attack the fort that very night.
Abul Hasan's army fights Khusrau's fractured army and sends them packing. Nisa comes up with a plan to disintegrate Khusrau's army and succeeds in doing so. Ghiaz Beg escapes from the fort and lets Jehangir know about Khusrau's crumbling army.
Khusrau abandons his army but is captured by Jehangir. The father asks his son how he wishes to be punished. Khusrau asks his supporters to be punished but begs for mercy to be showed on him. Jehangir has him walk along a street lined with impaled bodies of his supporters, much to his shock. Jehangir and his entourage are welcomed at the Agra fort with much fanfare.
Jagat can't fathom the fact that her son is getting married to Nisa's niece. Mahabat asks for all official documents of the royal khazaana to be brought in and on studying the same, discovers discrepancies in Ghiaz Beg's dealings. Just as Jehangir contemplates Mahmud's future, Mahabat informs him about Ghiaz Beg. The king decides to look into these matters after the engagement. Mahabat shares the information with Jagat, who doesn't miss a chance to insult Nisa at Khurram and Arjumand's engagement.
Nisa sees her father take bribe and confronts him about the same. He admits to her that he has been in a bad financial state for a long time now, a point that Jagat drives home too in a heated argument between the two. Jehangir requests Nisa to meet him and when she does, tells her that he intends to ask Ali Quli to divorce her. When Ghiaz Beg is made to confess about the bribes he took, Jehangir says to him that all will be forgiven if he gets his son-in-law to divorce his daughter and Ghiaz Beg agrees.
Ali Quli refuses to divorce Nisa and announces that he will take on Jehangir. The king decides to send his trusted friend and advisor, Koka to Bengal to discuss the matter with Ali Quli. Jagat rants to Mahabat about their consistent failures at driving Jehangir and Nisa away from one another. As a last attempt at the same, Mahabat sends a letter to Ali Quli, informing him about Koka's arrival. The letter states that Koka will arrive in Bengal with murder on his agenda. What ensues is a bloody fight in which Ali Quli, Koka and Yasmin are killed brutally.
Nisa escapes with Laadli and Danish in tow. On the run in the wilderness, Nisa discovers that she is being chased for the death of Ali Quli. Jehangir orders his army to look for her as well. Beating all odds, Nisa reaches her house and visits Ruqaiyya at the earliest. Ruqaiyya dresses her up and presents her to Jehangir, whose happiness knows no bounds. Ruqaiyya also makes sure that the news about Nisa's arrival reaches Jagat and the two fiery women have some altercations. Jagat breaks down before Mahabat and insists that their game is up - she has lost her husband to the woman she has always only hated, Nisa.
Pasha Begum consipres against Nissa so as to disrespect her. Badshah comes and meets Nisa, and requests her to come to his palace, but Nissa declines as it would bring shame to her family. Badshah Jahangir thinks of how the nobles could allow the marriage and comes up with a strategy. Transfering and reconstructing the positions of nobles in the kingom, he makes sure they agree to his conditions, thus allowing him to unite with Nissa. Jahangir marries Nissa and brings her back to the palace with respect. He names her Nur Jahan and gets the royal coins inscribed with her name.