Mughals established their dominion in India, a legacy that began with Babur and continued through Humayun to Akbar, who uniquely was the first Mughal emperor born on Indian soil. The year is 1555, and following the unexpected demise of Humayun, Hemu (Shehzor Ali) claims the throne of Delhi. In this time of turmoil, Bairam Khan (Yuri Suri), a steadfast general of the Mughal empire, stands beside the young Emperor Akbar. With Hemu commanding an army twice that of the Mughals, Bairam Khan devises a strategy to eradicate Hemu in battle, and this ambitious plan ultimately succeeds at the Battle of Panipat. In a gruesome turn of events, Bairam Khan beheads Hemu following Akbar's refusal to stain his hands with blood.
With this crucial victory, Bairam Khan embarks on consolidating the vast Mughal empire, dispatching emissaries to kings across Hindustan with a mandate: surrender your treasury and pay taxes to the Mughals or face their formidable wrath. While some rulers comply, many outright reject these demands. As a young emperor, Akbar (Hrithik Roshan) leads his armies valiantly yet consistently refuses to execute vanquished kings, even standing against Bairam Khan on this principle. Akbar aspires to govern Hindustan with compassion and justice, a vision that resonates with the defeated kings, compelling them to accept Mughal rule amicably. Eventually, Akbar relieves Bairam Khan of his duties, sending him on a pilgrimage to Mecca.
In a twist of fate, Jodhaa (Aishwarya Rai Bachchan), the daughter of Raja Bharmal (Kulbhushan Kharbanda) of Amer, finds herself betrothed to Rajkumar Ratan Singh (Aman Dhaliwal) of Ajabgarh. Raja Bharmal proclaims his son Bhagwant Das (Digvijay Purohit) as his successor, overlooking Jodhaa's cousin Sujamal (Sonu Sood), whom Jodhaa wishes to see as the rightful heir instead. Bitter over this injustice, Sujamal seeks refuge with rebel leader Sharifuddin Hussain (Nikitin Dheer), who eyes Delhi itself, despite being Akbar's brother-in-law and the governor of three provinces.
As tensions rise, Raja Bharmal proposes a peace treaty through the marriage of Jodhaa to Akbar, successfully circumventing conflict. Understanding the significance of such an alliance for the empire, Akbar consents, as it would pave the way for a united Hindustan. However, this arrangement upsets the existing partnerships among the kings of Rajputana and brings Jodhaa's wishes to marry Ratan Singh to naught. Distressed by being treated as a mere pawn in a political game, Jodhaa pens a desperate letter to Sujamal but ultimately refrains from sending it. Sharing her plight with her mother, Rani Padmavati (Suhasini Mulay), she receives a vial of poison as insurance against her impending marriage.
Determined to retain her Hindu faith post-marriage, Jodhaa confronts Akbar, demanding concessions that he surprisingly grants. Following their wedding, she maintains a facade of resistance, while Akbar assures her that time will heal all. Upon her arrival at Agra fort, tensions simmer when Akbar’s nurse, Maham Anga (Ila Arun), plots to undermine Jodhaa, while the mughal finance minister Todar Mal (Pramod Moutho) finds himself at odds with the court's religious leaders over Jodhaa's newly established temple, meant to honor her beliefs.
As political maneuvering continues, Akbar and Jodhaa gradually discover mutual respect and admiration for each other. During a Rajputana feast held in Jodhaa’s honor, she insists on preparing the meal personally, providing a moment of levity amid court intrigues. When yet another dark betrayal strikes the court, leading to the assassination of the prime minister at the hands of Adham Khan (Shaji Chaudhary), Akbar is forced to confront treachery from within his own ranks. Outraged by Adham's actions, Akbar ultimately settles old scores with justice being his preferred weapon.
Adding to the chaos, Sharifuddin aligns with opponents of Akbar, setting the stage for conflict. As Jodhaa's character comes under scrutiny, misunderstandings lead to her temporary banishment from the court. Yet, when the truth eventually surfaces, Akbar seeks to reconcile, enabling Jodhaa’s return. Their relationship flourishes as they engage in spirited discussions and sparring matches, painting a vibrant picture of their union.
Realizing the need for peace, Akbar boldly proclaims religious tolerance, earning Jodhaa’s admiration and trust. But the peace is short-lived, as Sharifuddin instigates his own foul play, attempting to assassinate the emperor—an endeavor that injures Akbar but fails to eliminate him. When the threat escalates toward Jodhaa and the empire, Sujamal steps in heroically, only to meet an untimely demise while trying to warn Akbar. As the fate of Hindustan hangs in the balance, Akbar triumphs over Sharifuddin, but mercy prevails and he spares his life for familial ties.
In the final reckoning, Akbar unveils his vision for a harmonious empire where every religion is honored, thereby establishing a thriving community rooted in respect. The story culminates with the acknowledgment of Akbar and Jodhaa’s enduring love, a legacy rich in compassion that, sadly, fades from the annals of history.
