Identity Crisis and Countdown
In the 2004-05 limited series Identity Crisis, Jean Loring kills Sue Dibny, the wife of the Elongated Man. After stealing some of the Atom's shrinking technology and his costume, she kills Sue in a misguided attempt to win Palmer back. She also arranges a hit on Tim Drake's father Jack Drake, which is carried out by Captain Boomerang (Digger Harkness). The intent is for Jack to kill some random attacker, but both manage to kill each other. After committing her to Arkham Asylum, Palmer shrinks himself to microscopic size and disappears.
Palmer eventually meets up with his old friend Carter Hall after microscopically traveling through phone lines. He warns Hall of the consequences of mindwiping Batman and of harassing criminals over a crime that is perpetrated by Jean, one of their own. Palmer explains he needs time away, and shrinks himself again after Hall agrees to keep the meeting secret.
His legacy lived on, however. Ryan Choi, a student of physics in Hong Kong who corresponded with Ray Palmer via mail in the past, found a copy of his costume and shrinking device to become the current Atom. Around this same time, an unnamed teenager with powers similar to Palmer joins the Teen Titans under the name Molecule. After a brief tenure with the team, he is later killed during a confrontation with the Terror Titans.
During the missing year, Palmer's technology is employed by Supernova to shrink and grow in size to enter and exit the bottle city of Kandor.
DC Comics would not reveal Palmer's whereabouts since his disappearance at the end of Identity Crisis. However, Palmer returned to play a very important role in the Countdown limited series. A Monitor asks the Source Wall what is the solution to "the great disaster," it answers "Ray Palmer". Subsequently, Kyle Rayner, Donna Troy and Jason Todd scour the multiverse for the former Atom, who may hold the key to saving reality from a crisis of unparalleled proportions.
In their travels, the quartet has found people marked with the Atom's familiar symbol. The group tracks Palmer to Earth-51, where he assumes the life of its native Palmer after his life is cut short during his studies of the multiverse and discovery of the looming Crisis. Meeting the Jean of Earth-51 and the Justice League again for the first time, Palmer is found on a world where the heroes have been able to eradicate supercrime and create a utopian Earth (later revealed to have been the result of this reality's Batman murdering all of this world's super-criminals after the Joker killed Jason Todd). However, once Kyle, Donna, Jason and Bob the Monitor are able to track him down, Bob attempts to kill Palmer; with the Challengers' help, Palmer escapes and reveals to the Challengers that it was the Ray Palmer of Earth-51 who was meant to stop the Great Disaster and that he had been trying to carry on his work, to no avail.
When the Challengers return to their own Earth, Jimmy Olsen is kidnapped by Mary Marvel, who has been corrupted by Darkseid. Palmer hitches a ride from within Jimmy. When Darkseid takes control of Jimmy's powers, Palmer locates and shuts down the control sphere inside Jimmy's brain, but is then swarmed by Apokoliptian antibodies. While escaping this onslaught, Palmer discovers the "battery" containing the New God spirit energies. Palmer removes it from Jimmy's head and shatters it, releasing the energy.
Palmer later (after much cajoling) joins Donna, Kyle, and Forager in their new mission as border guards to the multiverse, realizing that there is nothing left for him on Earth. However, Palmer returns home to New Earth one more time, upon realizing that his old nemesis Chronos had taken his identity to mislead a young pretender to his identity, Ryan Choi. After helping his successor to once again save Ivy Town, he returns to the multiverse with a new sense of fulfillment, leaving his town in the hands of a new, capable hero.
During the Final Crisis, Palmer returns to New Earth and works with Choi again to aid in the efforts to evacuate the last free humans.
In the Justice League: Cry for Justice mini-series, Palmer joins Hal Jordan's Justice League.