Kirk is now in a space suit and has exited the ship. The aperture in front of the Enterprise opens, and Spock's unconscious body floats toward him. Later, Dr. Chapel and Dr. McCoy are examining Spock in sickbay. Dr. McCoy performs scans and determines that Spock endured massive neurological trauma from the mind-meld.
Spock tells Kirk he should have known and Kirk asks if he was right about V'Ger. Spock calls it a conscious, living entity. Kirk explains that V'Ger considers the Enterprise a living machine and it's why "Ilia" refers to the ship as an entity and the crew as an infestation.
Spock describes V'Ger's homeworld as a planet populated by living machines with unbelievable technology. But with all that logic and knowledge, V'Ger is barren, with no mystery or meaning. He momentarily lapses into sleep but Kirk rouses him awake to ask what Spock should have known. Spock grasps Kirk's hand and tells him "This simple feeling is beyond V'Ger's comprehension. No meaning, no hope. And Jim, no answers. It's asking questions. 'Is this all that I am? Is there nothing more?'"
Uhura chimes in and tells Kirk that they are getting a faint signal from Starfleet. The intruder has been on their monitors for a while and the cloud is rapidly dissipating as it approaches. Sulu also comments that the intruder has slowed to sub-warp speed and is three minutes from Earth orbit. Kirk acknowledges and he, McCoy and Spock go up to the bridge.
Starfleet sends the Enterprise a tactical report on the intruders position. Uhura tells Kirk that V'Ger is transmitting a signal. Decker and "Ilia" come up to the bridge, and she says that V'Ger is signaling the Creator. Spock determines that the transmission is a radio signal. Decker tells Kirk that V'Ger expects an answer, but Kirk doesn't know the question.
Then "Ilia" says that the Creator has not responded. An energy bolt is released from V'Ger and positions itself above Earth. Chekov reports that all planetary defense systems have just gone inoperative. Several more bolts are released, and they all split apart to form smaller ones and they assume equidistant positions around the planet.
McCoy notices that the bolts are the same ones that hit the ship earlier, and Spock says that these are hundreds of times more powerful, and from those positions, they can destroy all life on Earth. "Why?" Kirk asks "Ilia." She says that the carbon unit infestation will be removed from the Creator's planet as they are interfering with the Creator's ability to respond and accuses the crew of infesting the Enterprise and interfering in the same manner.
Kirk tells "Ilia" that carbon units are a natural function of the Creator's planet and they are living things, not infestations. However "Ilia" says they are not true life forms like the Creator. McCoy realizes V'Ger must think its creator is a machine.
Spock compares V'Ger to a child, and suggests they treat it like one. McCoy retorts that this child is about to wipe out every living thing on Earth. To get "Ilia's" attention, Kirk says that the carbon units know why the Creator hasn't responded. The Ilia probe demands that the Creator "disclose the information."
Kirk won't do it until V'Ger withdraws all the orbiting devices. In response to this, V'Ger cuts off the ship's communications with Starfleet. She tells him again to disclose the information. He refuses, and a plasma energy attack shakes the ship. McCoy tells Spock that the child is having a "tantrum."
Kirk tells the probe that if V'Ger destroys the Enterprise, then the information it needs will also be destroyed. Ilia says that it is illogical to withhold the required information, and asks him why he won't disclose it. Kirk explains it is because V'Ger is going to destroy all life on Earth.
"Ilia" says that they have oppressed the Creator, and Kirk makes it clear he will not disclose anything. V'Ger needs the information, says "Ilia." Kirk says that V'Ger will have to withdraw all the orbiting devices. "Ilia" says that V'Ger will comply, if the carbon units give the information.
Spock tells Kirk that V'Ger must have a central brain complex. Kirk theorizes that the orbiting devices are controlled from there. Kirk tells "Ilia" that the information cant be disclosed to V'Ger's probe, but only to V'Ger itself. "Ilia" stares at the viewscreen, and, in response, the aperture opens and drags the ship forward with a tractor beam into the next chamber.
Chekov tells Kirk that the energy bolts will reach their final positions and activate in 27 minutes. Kirk calls to Scotty on the intercom and tells him to stand by to execute Starfleet Order 2005; the self-destruct command. A female crewmember asks Scotty why Kirk ordered self-destruct, and Scotty tells her that Kirk hopes that when they explode, so will the intruder.
The countdown is now down to 18 minutes. DiFalco reports that they have traveled 17 kilometers inside the vessel. Kirk goes over to Spock's station, and sees that Spock has been crying. "Not for us," Kirk realizes. Spock tells him he is crying for V'Ger, and that he weeps for V'Ger as he would for a brother.