Every story has a beginning, and sometimes those unfinished bits of the past can come back to haunt the present. What could cause a metahuman to hold a grudge against the world?
Ms. Oberon, teacher of the Rainmaker Program at PS238, attempts to get everyone in her class to calm down and back in their seats. One of her students, Lyle, wants to give a history presentation, just like the other students got to a few weeks ago. The students are confused; some of them thought Lyle wasn't even able to speak. Before Lyle can begin his report, Zachary pops up from an underground tunnel. He was helping Herschel and Zodon lay some cables under the school. Once Zachary takes his seat Ms. Oberon re-introduces Lyle to the class. Lyle can see patterns in the world around us and can deduce great amounts of information from these observations. So much so that it's painful to the point of causing him to pass out. As such, Lyle spends most of his time in a white room listening to music. He came out of his white room to give his report because if he didn't, bad things would happen. Ms. Oberon encourages him to start his report, on the original Rainmaker Project.
Lyle recounts the events of the past. The original Rainmaker Program was started in 1960 and had one person in it, Harold Nelson. Harold was gifted with the ability to manipulate weather and cause it to rain or stop raining. He was also the first person with powers that the government could safely study. Every other metahuman before him was too dangerous to contain. The government hoped they could find out where super powers came from.
In an attempt to further the study of Harold's abilities, the government made a deal with the cyborg super-villain Doctor Irons, who was incarcerated for bank robbery. Doctor Irons had metatechnologist abilities and the ability to create devices decades ahead of their time. Using the government's funding he built a machine that was supposedly similar to an MRI. This device was to be used to scan Harold's body and brain as he used his powers. In reality the machine was designed to temporarily enhance the abilities of young Harold. As Harold lay on the bed of the machine, Doctor Irons uses his robotic voicebox to generate subliminal-level sound and communicate with Harold. He tells Harold that the story of Harold being an orphan is a lie and that his parents don't even know he is alive. He compounds this by enticing Harold to want to escape from the prison the government has created for him. Using his machine he boosts Harold's powers to the point where Harold is able to generate an enormous thunderstorm outside the building. This thunderstorm is able to generate massive bolts of lightning and one blows a hole in the wall of the test chamber. Harold notes that he can't make the storm stop, to which Doctor Irons replies that was the idea. As Doctor Irons makes to leave, a stray bolt of lightning blows his body to pieces, causing his head unit, which encases his brain and is still functioning, to land on Harold's lap. Harold makes a run for it with Doctor Irons' head in hand. As they run, Harold notes that they should stay away from running water and high places. He notes this just as a wall of water from a flash-flood comes bearing down upon them.
Much to Harold's surprise, he is rescued at the last second by a young Ul-Ron Peterson, who will someday become the hero known as Atlas. Ron swoops down and carries Harold up into the sky, bearing him safely to the Peterson farm. Ron's father chides him for "showing off" and reminds him that the fewer people that get a clear look at him the better. Mr. Peterson tells Harold he can stay at the farm if he pulls his weight. He also notes the head of Doctor Irons, which he takes to be some kind of modern art, and places in Ron's room. Ron then begins to show Harold around the farm and explain his chores to him.
Later that evening Harold and Ron are resting on the porch, discussing the work of the day. Ron explains to Harold that he can fly, lift heavy things, and can't be hurt. He takes Harold to the nearby barn and shows him the spaceship that brought him to Earth. Mr. Peterson discovers this and yells at Ron, sending him to his room without supper. He then swears Harold to secrecy, says that he hopes Harold likes it there, and notes that it'll be good to have someone else around that can feel an honest day's work in their bones. This angers Ron, who has been listening from the roof of the barn. He flies back into his room, muttering about how he's not his father's favorite anymore. Doctor Irons speaks to Ron, enticing him to believe that he can help Ron get rid of his "inconvenience" in exchange for access to certain machines and tools from the farm.
The next morning Ron and Harold are over a mile from the farmhouse, ostensibly to mend fences on the south pasture. In reality, Ron has retrieved the Project: Rainmaker sign from the ruins of the compound and tacked it up on one of the fence posts. He has also placed Doctor Irons' head on top of a scarecrow nearby. Ron accuses Harold of hiding his own secrets. Doctor Irons eggs him on, telling him that Harold is a criminal and subliminally telling Ron that Harold is a liar, wants to confuse him, steal his father, and destroy the farm.
As Ron moves to incapacitate Harold, Harold reflexively activates a previously unseen power and disables Ron's abilities. He then says that Ron's father love Ron and if Harold has to leave to make sure things don't get messed up then he will. Harold takes Doctor Irons' head down from the scarecrow, makes it start to rain, and then leaves Ron lying there on the ground.
The story flips back to the present at this time. Lyle notes that Ron never saw Harold again but while he was lying in the mud something else happened. At that point his presentation is interrupted by Ms. Kyle, who needs to talk to Ms. Oberon. Lyle knew Ms. Kyle would be there and he needed to finish his report when the teacher couldn't hear because certain people needed to know certain things, otherwise bad stuff would happen.
Lyle continues. Ron is still sitting in the mud when Tom Davidson appears from a time warp behind him. Tom explains to Ron that everything is going to be fine. Ron's power loss is only temporary and he'll be back to normal in half an hour. Harold will be ok eventually and Ron only did what he did because Doctor Irons was able to get inside his head with his voice trick. Ron says that his dad is going to be really mad. Tom gives him a note to give to his father that he says will explain everything. Ron questions why he'll believe this, and Tom says he was the one that convinced Ron's father to adopt him. Tom then notes that he has to wait for someone. Within a matter of seconds Zodon appears from a time warp, with Tyler Marlocke and a school desk in tow. Zodon curses at his timeslip device and then disappears again, leaving Tyler and his desk behind in the rainstorm. Tom greets Tyler, welcoming him to August twelfth, 1966. Tom introduces Tyler to Ul-Ron, noting that someday he will become Atlas. Ron asks who Atlas is and how Tom knows his whole name. Tom says that Ron will see. Tyler asks about Zodon, to which Tom replies that they'll deal with him soon enough, and then he reminds Ron to give the note to his father. Tom says they'll say "hi" to Ron's son for him, they say their goodbyes, and then disappear through a time warp.
Lyle wraps up his report by noting that Harold made his way west, holding several jobs and getting an education. He later sued the government and won some money, and is still alive. He also notes that Harold has heard about the new Rainmaker Program and is going to come to the school, but has a way to go yet.
Several weeks later, we see a van entering a small town in Missouri. A bearded man with a wide-brimmed hat steps out and talks to the people of the town, saying that the rainmaker has come. He then causes it to rain and asks them for the fee he was promised when they spoke on the phone. The townspeople can't pay him, but they do let him fill up his gas tank. Harold climbs back into the van and talks to Doctor Irons' head, which is still functional. Doctor Irons is pushing him to continue their mission, Operation: "Rainmaker Rescue", so they can keep the kids from suffering the same fate as Harold did. But does Doctor Irons have ulterior motives?