Damnit Morpheus, not everyone believes what you believe!"
"My beliefs do not require them to.—Jason Lock and Morpheus, The Matrix Reloaded
Morpheus is a Zion operative who serves in the city's defense force against attack from the Machines. His hovercraft, the Nebuchadnezzar, is smaller than most, and has far less armament than its sister craft. As with all hovercraft, the "Neb" is equipped with an EMP weapon to disable any sentinels that they encounter.
Morpheus (the name of his persona while a bluepill within the Matrix is unknown) is an even-mannered man with a personality that commands respect in many who encounter him. As a result of his belief in the Prophesy, Morpheus devotes "all of his life" in search of The One, the human who will bring an end to the Machine War. Morpheus has become a spiritual figure to many citizens of Zion, much to the consternation of others who don't believe in the Prophesy, such as the natural-born commander of the Zion defense force, Jason Lock.
The Search for NeoEdit
Neo, you may have spent the last three years looking for me, but I have spent my entire life looking for you.—Morpheus, The Matrix
Morpheus somewhat detaches from life within Zion after the Oracle predicts that Morpheus will find The One, leaving close relationships such as that with Niobe, the finding of The One his all-consuming passion.
The day comes when Morpheus does find a bluepill named Thomas Anderson, who calls himself normally by his hacker name of Neo. Through some misfortune, Morpheus is honored to meet the potential savior of mankind, offering Neo a red pill to find out more about the Matrix, or a blue pill to return to his old life. Neo's choice leads him out of the power plant, where Morpheus has time to repair and rebuild Neo's pod-weakened body before he must tell him the truth of the world as he knew it.
Neo reacts badly to the truth of the Matrix, and Morpheus apologizes for the event, indicating that there is normally an age limit to freeing minds that he had to break in order to free Neo. He also explains the Prophesy to Neo, and Neo's role in it.
Shortly after Morpheus and Neo return from his first visit with the Oracle, Cypher's plan to betray the crew in an effort to return his body permanently to the Matrix is launched. All of the ship's crew are killed except for Neo, Trinity, and Tank. Morpheus attacks their pursuers in order to save Neo from capture, but is captured himself by Agent Smith and taken to a military stronghold for interrogation.
Morpheus is drugged to crack his mind into giving the codes to the Zion mainframe. Aboard the Nebuchadnezzar, Tank recommends killing Morpheus by pulling his headjack in order to keep Zion's secrets safe. Neo stops Tank, remembering the prediction the Oracle gave to him: Neo must choose to save himself or Morpheus from death. Trinity and Neo reenter the Matrix in a very dangerous mission to rescue their leader. They are successful, and Morpheus and Trinity manage to escape.
But Neo remains unable to immediately leave and is attacked by Agent Smith. Instead of running from the virtually unstoppable agent, Neo stands his ground, much to the fascination of Morpheus. But Neo is not able to withstand Smith's relentless attack, and flees, dodging Agents Brown and Jones as well as Smith. Morpheus, his ship under attack itself by sentinels, arms the EMP and whispers words of encouragement to Trinity, but when Neo is apparently shot and killed just moments away from a hard line and escape, Morpheus is crestfallen.
Trinity is not finished yet. She tells the lifeless body of Neo of her prediction from the Oracle: She would fall in love with The One. Concluding that Neo cannot be dead, she kisses him, and Neo's life signs return strongly. His avatar stands up again in the Matrix, enlightened to his powers as The One, and soundly defeats the retaliating agents.
Morpheus is happy to serve with Neo through many adventures, freeing more minds from the Matrix in their first six months after Neo's transfiguration. When several hovercraft crews receive word through another ship, the Osiris, that the Machines are planning a massive attack against Zion, Morpheus is unpeturbed. He asks for one ship to stay within the Matrix to await further instructions from the Oracle, thereby directly disobeying Commander Lock's orders to return to Zion.
After Neo's Death, Morpheus returned to the Matrix to consult with the Oracle on the subject of Neo's remains. He then proceeded to meet with Redpills to show them that he was reconstructing Neo's RSI. After the reconstruction failed he began to challenge the machines to give Neo's remains to Zion. Later Morpheus gained access to Code Bombs and used them to cripple the Matrix.
When Morpheus was setting up a code bomb in Westview, he noticed a fly buzzing from his only exit. It seemed as though he anticipated that The Assassin would be there, even though the Assassin was never seen in public until that point. It seemed like Morpheus escaped by using a back door to the building. As he walked out a vent the size of a bread box opened and the Assassin squeezed out of it, plugging several holes into Morpheus. Morpheus's body was on display in the Sobra Shores Church where it burst into flies on several times every hour. However, recently broadcasts by him have been seen around the Matrix, and has lead to the conclusion that he is not in fact dead.
It was later discovered that Morpheus was not in fact killed, but the bullets used by the Assassin were used to jam his transmission, preventing him from broadcasting inside the Matrix. Upon a fractured broadcast March 30th, 2007, he told the large gathering of Merovingian, EPN, Zionite, Cypherite, and Machinist redpills that Neo was in fact alive, being held hostage in the Machine City. Nothing has come along to corroborate this story, but Morpheus encouraged those present to fight against the Machines, and make ready for a war.
It is also theorized that these transmissions are being made by The General as a form of a diversion used to spread fear and mistrust of the Machines by using remnants of Morpheus's RSI left in the system.