Online
Although the fate of Neo was never truly revealed in the MMORPG sequel, The Matrix Online, his influence nevertheless had a strong impact on several key events throughout the game.
In the beginning, scattered code fragments of Neo's "RSI" (Residual Self Image) were found on the bodies of the impostor Agents who appeared across the Mega City during Chapter 1.1 (later revealed to be Sentinels under the command of The General program). When held, these fragments echoed some of the final thoughts of Neo inside the redpill's mind. Each of the three main post-war political organizations inside the Matrix realized the possible significance of these fragments and began fighting amongst themselves to gather as many as they could.
The Oracle reveals a secret society of exiles known only as the Shapers, who are the only ones able to bring the Fragments together in any significant way and that they must be protected from the impostor agents' corruption. The redpills' distrust and organizational differences prove too much for any strong unity, so that a Shaper fell into the captivity of the false agents. His power was used to encode some part of The One's being onto them, creating the powerful, pale-skinned "N30 Ag3nts".
In Chapter 1.2, Morpheus states that though the Machines never returned Neo's physical remains (Neo's body in the real world) to Zion, they did not "recycle" them: a reference to the first film, in which Morpheus tells Neo that the machines liquefy deceased occupants of the Matrix to provide organic sustenance for its living inhabitants. This would be the driving force behind Morpheus' descent into fanatical terrorism against the System in an attempt to force the Machines to reveal Neo's fate, ultimately leading to his assassination.
The subject of Neo then fell to the side lines for other struggles until the arrival of The Oligarchs in Chapter 9. The original intruder, Halborn, was notably intrigued by the life of The One and was personally shocked about the implications of Neo's ability to affect Machines outside of the simulation had on his search for what he called "The Biological Interface Program".
After Halborn's removal in Chapter 10, little more was questioned until the revelation of the Trinity project, originally headed by The Oracle, in Chapter 12. It was revealed that both Neo and Trinity were actually the culmination of decades of Machine research into translating human DNA perfectly into Machine code, allowing them to interface directly with technology without the need for simulated interfaces.
Read more about this topic: Neo (The Matrix)