Years had passed, and Morgana finally accepted what happened with Smith, forgiving herself in the process. She had been naïve, doubted herself, and ignored her gut, but never again. Now, she would take the time to really know someone well, and verify their intentions. With a new perspective in life, and better knowledge about people, she met another doctor while in Zion's medical school, and married him. Tending to the sick and wounded of Zion, the pair had three children.
Natasha continued to fight in the war to liberate minds, and was quite successful at it. Having known Marcus for a long time, she finally gave him a chance, and the two began a relationship. Continuing to rise in rank, Natasha became quite popular in Zion for her personality and bravery.
Jet had a little boy of her own that resembled exactly her little brother, Orion and the crew continued their journeys with Natasha, and Captain Ulrikson retired, promoting Harker to take his place.
In the Matrix, Agent Smith became privy to a new assignment—hunting down a new Potential named Trinity, who was involved with Morpheus, and was one of the most infamous hackers in the world. A new day began, and Smith, donning his black sunglasses, walked back into the city, with unshakable resolve to smite the Resistance once again.