Trinity talks about Neo, but isn't sure if the line is secure. Agent Smith bitches out a lieutenant for not waiting for backup. Trinity kills the lieutenant's entire team. (#1, 1-22)
Agents chase after Trinity. She escapes but the agents don't care as they know the next target is Neo. (#2, 23-35)
Neo awakens to a knock at the door and strange messages on his computer screen. A group of friends buy hacking software from Neo and convince Neo to go out clubbing with them. (#3, 36-63)
Trinity introduces herself to Neo at the club. She tells Neo he's in danger and she knows what Neo is looking for. The answer will find Neo if he wants it to. (#4, 64-87)
Neo gets bitched out by his boss for being late to work. Morpheus calls Neo and tells him agents are there for him. Neo follows Morpheus's instructions to escape, but gives himself up when he thinks he might fall to his death. (#5, 88-129)
Agents interrogate Neo. They want Neo to help bring in Morpheus, but he refuses. Neo's mouth disappears and the agents insert a tracking robot into Neo. (#6, 130-155)
Morpheus calls Neo and asks if he still wants to meet. At the meet up, the tacking robot is removed which freaks Neo out as he thought he was dreaming. (#7, 156-186)
Neo finally meets Morpheus. Morpheus knows Neo feels something. They talk about the matrix. That it hides the truth of our slavery. But to know, Neo must see it for himself. (#8, 187-221)
Neo is given a choice to take the blue pill or the red pill. Neo takes the red pill and goes into shock before waking up for the first time. (#9,222-246)
Neo finally awakens and his body needs strengthening. There's talk about hope that Neo really is The One. Neo is told it's around the year 2199. Neo sees the hovercraft and meets the rest of the crew. (#10, 247-271)
Neo goes inside The Construct with Morpheus. They talk about what is "real". Neo is shown the world he knew and then the real world. Neo is told about the war between man and machines. Man blocked out the sun, so the machines used human bodies as a replacement enery source. The matrix keeps the humans unaware of this. Neo freaks and wants out. (#11, 272-324)
Neo can't go back. Morpheus apologizes for freeing Neo at such a late stage, but he had to. Neo learns of the Oracle and the prophecy. (#12, 325-341)
Neo meets people without plugs and learns about Zion. Tank is excited about Neo's potential. Neo starts combat training and loves it. Goes for 10 hours straight. (#13, 342-363)
Morpheus and Neo are in the sparring program. Morpheus explains what to expect and they fight. Morpheus wins, and tries breaking Neo's mind free of its imagined limitations. Neo's brain patterns are off the charts. (#14, 364-387)
Tank loads the jump program. Nobody has ever made it on their first try. Neo fails too, but there is something special about him. Neo learns he can die in the matrix. (#15, 388-404)
Morpheus tells Neo how people still plugged into the matrix are potential enemies. The girl in the red dress becomes an agent. Neo learns that eventually someone must fight the agents, and everyone who has tried so far has died. But their abilities are based on rules, so The One will succeed where others have failed. (#16, 405-433)
The ship is under attack from squid like machines called sentinels. The only defense is an EMP. The ship hides in the city sewer system. (#17, 434-447)
Neo sees the matrix on screen. Neo drinks liquor and is asked if he knows why he was brought into the real world. Neo is advised that if he sees an agent, he should run away as fast as he can. Cypher makes a deal with the agents to turn over Morpheus in return for being put back into the matrix. (#18, 448-486)
Breakfast time has a discussion about taste, and if the matrix got it right. Mouse tries to pimp out the red dress girl from the training program. Morpheus announces he's taking Neo to see the oracle. (#19, 487-514)
Neo is off to see the Oracle. He sees things from a past that never happened and is somewhat confused. Neo asks what the Oracle told Trinity and Morpheus and if she's ever been wrong. Neo meets another potential who appears to be bending a spoon. (#20, 515-547)
Neo meets the Oracle. She tells Neo he's not The One, but he will someday need to choose between his life and the life of Morpheus. (#21, 548-605)
Neo sees a déjà vu, which is a glitch in the matrix. They're under attack. They get plans for the building so they can find a way out. (#22, 606-626)
The agents are in the walls. Morpheus sacrifices himself to save Neo. (#23, 627-636)
Cypher exits first, saying he was in a car accident. Morpheus is alive and being moved. Cypher kills the operator and tells Trinity how he loved her and that he's tired of the real world. Cypher is going back into the matrix, and now he's about to kill Switch. (#24, 637-683)
Now Cypher is about to kill Neo, so he asks Trinity if she still believes Neo is The One. Cypher is killed before he unplugs Neo. (#25, 684-698)
Agent Smith tells Morpheus about the first matrix and why it was redesigned. The agents try to crack Morpheus's mind to get the mainframe codes. It is only a matter of time. There's talk of killing Morpheus before he gives up the codes as they are too important. Because of his talk with the Oracle, Neo decides to try and save Morpheus. Trinity is going too. (#26, 699-770)
Agent Smith compares humans to viruses. A disease on the planet. Neo prepares for battle. The Agent tells Morpheus he hates the matrix and needs the codes to be free. (#27, 771-804)
Neo enters the lobby, guns blazing. They command a helicopter and rescue Morpheus. (#28, 805-827)
Morpheus tells Neo he knew that Neo was The One. Neo says the Oracle told him he wasn't, but Morpheus says he was only told what he needed to hear. Morpheus and Trinity exit, but an agent shows up before Neo can get out too. Sentinels are coming while Neo and the agent fight. (#29, 828-852)
Neo and the agent continue fighting. Neo's signal is lost. The EMP is charged, but can't be used until Neo gets out. Neo gets instructions on a new exit. (#30, 853-879)
Neo appears to die, but Trinity's love brings him back. Neo is The One. Neo tells the agents he's going to show the people a new world without them. A world where anything is possible. (#31, 880-900)