For those that actually follow the storyline for the Matrix Online, here's some info.
Since the truce, Morpheus has tried to force the machines to give up Neo's 'remains.' In an effort to do so, he went on a crusade to have as many redpills as possible to strain the system. Eventually, the machines would surrender Neo's remains.
Fake agents with red eyes invade the Matrix. Even more alarming is the fact that some carry fragments of ... Neo. To be more accurate Neo's memories. Read the list.
People speculate that these agents are a by product of Agent Smith since both Neo and Smith merged and were shattered to bits. Some even claim gathering all the fragments will bring Neo back. (I doubt it.)