Clooney, who left the show in 1999 to pursue movie stardom, reprised his character Dr. Doug Ross. Now in Seattle, Ross works with wife Carol Hathaway (Julianna Margulies) to persuade a grandmother played by Susan Sarandon to donate the organs of her grandson.
One of those organs, the kidney, went to "some doctor in Chicago," Hathaway said. Neither she nor Ross knew the transplant patient was their old colleague John Carter, played by fellow "ER" original Noah Wyle.
The finale of the NBC drama is scheduled for April 2.
Once television's most popular show, "ER" anchors a diminished NBC lineup with about one-quarter the audience it had during its peak. Next season, NBC will replace it with Jay Leno.
Thursday's episode, written and produced by "ER" executive producer John Wells, was a reminder of the show's glory days and perhaps an era of network television that is gone for good.
"Let's hope we didn't bring all of these people out here for nothing," Clooney's character said to a group of people waiting to transport donated organs. He may as well have been speaking to audience members tuning in to "ER" for the first time in years.
The show even poked fun at its revolving door of actors since the original cast left. When Ross learned that two of the people waiting for organs were from his old County General Hospital in Chicago, they questioned each other on colleagues each might have worked with. There were few matches.
As he waited for a transplant, Wyle's character was visited by Dr. Peter Benton, played by Eriq La Salle. Benton tormented Carter back in the day, but this time stood by him and watched his surgery, saving Carter from trouble caused by an impatient surgeon.
"You stayed here," Carter said upon waking from the surgery.
"I didn't want to miss all the fun," Benton said.
During its peak, in the 1995-96 season, "ER" was the most popular show on television and averaged 32 million viewers a week. To put that in perspective, only one entertainment program — ABC's broadcast of the Academy Awards — has gathered more than 32 million viewers this entire season.
"ER" was TV's No. 1 show for three seasons and, as late as 2000-01, was the top-rated scripted series after fare like "Survivor" and "Who Wants to Be a Millionaire."
This season, "ER" is limping along in 49th place, averaging 8.2 million viewers an episode, according to Nielsen Media Research.
Besides Clooney and Marguiles, other old favorites from the show's heyday have paid respects with returns this season.
Anthony Edwards, who played Dr. Mark Greene, returned even though his character had been killed off: He appeared in a flashback scene. Laura Innes, who played Dr. Kerry Weaver from the second season through 2006-07, made a guest appearance, as did Sherry Stringfield, Alex Kingston and Paul McCrane.
Clooney had led the parade of series originals out the door. Margulies left in 2000, Edwards and La Salle in 2002 and Wyle in 2005.