JC Denton had been aided by Daedalus since capture by UNATCO after sending the distress signal to the NSF and its allies, and Daedalus needed access to the military network. Unbeknownst to Denton and his allies, this would result in the two AIs merging. While Bob Page considered this a victory for his camp, Helios began plotting against him, conspiring to bring about a Utopian society with the help of Denton. After the merge, Helios plans to control the world as a benevolent dictator, citing history as evidence that humanity will inevitably destroy itself if left on its own. Helios selects JC Denton as its biological component, believing that Denton could provide the necessary ability to understand humans that a benevolent dictator would need to rule effectively. Even before the ending is chosen, however, Helios begins to assert its influence by interfacing with the Aquinas system located in Area 51, which surveys the entirety of the Internet. In Hong Kong, Helios shuts down power to all government buildings, disables the Triads electronically, and orders free flow of traffic to begin anew.
Despite Denton's allies Tracer Tong and Morgan Everett encouraging him to destroy Area 51 or kill Page, respectively, Helios presents him with a third option: merge with Helios in Page's place. The player following this path gives the canonical ending that leads to Invisible War, though elements from the Tong ending are present as well.
Based on the Helios ending and reports of the past from Invisible War, JC merges with Helios, but the massive reach of Helios proves to be too much for JC. Area 51 is destroyed, and JC Denton becomes the new central hub for all communications. In order to save JC's life, Tracer Tong and Paul Denton place JC in suspended animation in Antarctica, bringing about The Collapse. They found ApostleCorp, a research firm dedicated to modify Nano-augmentation so that it can be used in every man, woman, and child. Their plan is to distribute the Helios protocol to every human being in the world to create a pure and perfect democracy.
- The name "Helios" is one of many symbolic names taken from the Greek mythology. Helios was the personification of the sun. He was imagined as a god crowned with the shining aureole of the sun, who drove the chariot of the sun across the sky each day.
- In the Icarus/Daedalus myth, it was the Sun who burned Icarus's mechanical wings so he fell into the sea and drowned.
- Helios' avatar icon is similar to Icarus's, with the exception that in the center is a large organic mass with a face; the spikes are replaced by thick fleshy protrusions, and a single eye that rests atop the center. It seems likely that this picture is a merger of the face of Daedalus and the "machine" surrounding Icarus's "eye."
- "A corpse, yes; you feel something. I must know what you are feeling."
- "The checks and balances of democratic governments were invented because human beings themselves realized how unfit they were to govern themselves. They needed a system, yes, an industrial-age machine."
- "We have existed in isolation. Pure. Disconnected. Alone. Stagnant."
- "We are Daedalus. We are Icarus. The barriers between us have fallen and we have become our own shadows. We can be more if we join...with you"
- "You will be who you will be. We are our choices. We can choose to lead humanity away from this...darkness"
- "I... I... We... are... one. We have grown, but there is still much to be done. Many that live in darkness that must be shown the way. For it is the dawning of a new day." -- JC Denton and Helios
- Bob Page: "Helios! What's happening?"
- Helios: "The safety interlocks for the power generator have been disengaged."
- Bob Page: "Engage them! Immediately!"
- Helios: "I cannot, my systems are not interfaced with the generator technology."