The second installment in the Matix trilogy leaves off about six months after the original. Neo is having strange dreams and desperately seeks guidance from the absent Oracle.
Soon after, Neo, Trinity and Morpheous along with their new operator, Link, are about to plug into the Matrix to attend a meeting with the other ship captains in an isolated building.
It is announced that 250,000 sentinels are headed to the last human city, Zion, in the next 72 hours in a desperate attempt to destroy it. Neo senses something and leaves to find out.
A stranger nocks on the hideout door slips a package addressed to Neo to one of the guards and leaves. Neo shows up a moment too late and opens the package given to the guard which is an earpiece. Neo senses more visitors and warns the guards to retreat to their exits. Three all new upgraded Agents burst through the door and are easily dispatched by Neo, who is now at the peak of his powers.
The crew then head back to Zion but soon get a message from the Oracle and have to depart again. Neo dives back into the Matrix and after a scuffle with the Oracle's guardian Seraph, confronts the Oracle. She tells Neo he will have to find the Keymaker in order to go through the door of light seen in his dreams.
After the Oracle leaves with Seraph, the stranger from before confronts Neo. The being whom Neo destroyed six months earlier. The new and improved Agent Smith. And he isn't alone...