Nathaniel Black (loosely based on Joseph Louis Cook) is the half-Iroquois son of the late John Black from Act II in the previous game, raised by his mother Nonahkee and his uncle Kanyenke. The campaign opens as Nathaniel and Kanyenke are trying to discourage the Mohawk and the Seneca from fighting in the American Revolutionary War. However, they are ambushed by a group of Mohawks and head to an Oneida village nearby. From there, they counter-attack and destroy an enemy Town Center, thus causing their enemies to flee. When Nathaniel and Kanyenke return to their village, they find that the Mohawk and a group of Hessian mercenaries, led by Colonel Sven Kuechler, have raided the village and captured Nonahkee. They rescue Nonahkee, but Kuechler and his main army escape, leaving the Iroquois Confederacy dissolved.
Nathaniel's village supports the American colonists, and Nathaniel heads to Boston, where his men help defend a redoubt on Breed's Hill the British. After George Washington takes command, a series of defeats drives the colonials back across the Delaware River, where they are joined by Nathaniel. Here, Washington leads a small force, including Nathaniel, across the Delaware, where they attack a Hessian encampment at Trenton and defeat the rearguard of the army at Princeton. This is followed by another victory at the Battles of Saratoga, However, the army is once again defeated at Brandywine and Germantown and is forced to camp for the winter at Valley Forge, where they suffer greatly from the cold. This leads Nathaniel to use most of his family's fortune to supply the army throughout the winter.
The next scenario is the fictional battle of Morristown, where Nathaniel has his chance for revenge on Kuechler, who leads an attempt to destroy the capitol building of Morristown. Using artillery shipments he receives from Washington, Nathaniel sneaks around the Hessian flank and relieves Morristown. Refusing to accept defeat, Kuechler joins the fight with Nathaniel and is killed. After Kuechler's death, Nathaniel is said to have fought at Charleston, Camden, and King's Mountain.
As the tide begins to turn, the French join the war and help the revolutionaries gain a victory at the Battle of Yorktown, where Nathaniel is instrumental in capturing several redoubts. With the Revolution won, Nathaniel returns home a poor man having spent his family fortune on outfitting his volunteers and supplying the troops at Valley Forge. During the epilogue video of the campaign (where Nathaniel is at Yorktown), the "Old Coot" (secretly Morgan Black) from Act I and Act III in the previous game can be seen watching his great-grandson's victory.