In the VisionQuest season finale, The Client's identity is revealed, and thanks to a timely intervention from Speed (who finally meets his brother, Billy, via the Dreamscape), the villain is defeated.
Rejected, The Client guns down Jocasta with an Adamantium bullet and, in her dying moments, she frees Ultron and helps transfer his consciousness into Jo Carrington's nanobots. With a body now comprised of countless tiny robots, the super-powerful Ultron crushes his human avatar to death and, after Jocasta dies in his arms, he vows to wipe out humanity in revenge.
Vision, now back with his classic green and yellow appearance, battles Ultron and decides the best way to stop him is in the Mindscape. There, he tries to change Ultron's mind in "UltraVision," a sitcom not unlike the one the Avengers: Age of Ultron antagonist was seen watching in VisionQuest's opening episodes.
As Vision and Tommy attempt to stop Ultron from laying waste to London, we learn that Ultron actually saved F.R.I.D.A.Y. by showing her mercy. The grieving Ultron argues that he's doing the same for humanity by killing them, sparing people from experiencing what he's feeling.
Ultimately, Ultron seems unwilling to relent, but it doesn't matter; "UltraVision" was a means of keeping the villain distracted so that Vision could burn out their respective cores, killing them both. The nanostorm over London self-destructs; Vision is dead, and Ultron vanishes after sharing a tender moment with his son.
Tommy and Billy manage to bring their father back to life by combining their powers, and as the series wraps up, we see that Lisa Molinari and E.D.I.T.H. are working with the heroic Paladin now, and that they're travelling alongside Tommy to meet with Billy in New Jersey.
Speaking with his father, Tommy wonders whether they'll see Wanda Maximoff again, to which Vision points out that, as they've said goodbye before, it stands to reason they will say hello again.
As the finale wraps up, Vision says goodbye to his Mindscape as it's time for him to get out into the real world. However, as he's leaving the house, the phone rings. Ultron lives! Some of the nanobots were unaccounted for, and Ultron—now residing in The Client's manor—is undecided about his future. He may take in art or burn it all, but he knows he doesn't want to do it alone, and it's all thanks to Vision, "m'boy."
With that, Vision sets off on a new adventure, though a mid-credits scene sheds a little more light on what's next for Ultron. You can read about that here. As for the second stinger, that has to be seen to be believed.
While the VisionQuest finale doesn't directly set up Avengers: Doomsday, (well, not until the second post-credits scene, at least) it serves as a fresh start for Vision and sets the stage for him, Billy, and Tommy to seek out the Scarlet Witch and for Ultron to take on any number of roles in the MCU moving forward. Season 2 is definitely possible, but an adaptation of Avengers: The Children's Crusade may be an effective next step for all these characters.
VisionQuest is now streaming on Disney+.