Dragon Train Rebellion picks up the story two years after the end of Dragon Train (Book 1). Jaiden has returned to his father's farm in the village of Hilltop and both try to get along better but their poor relationship mostly returns to what it had been. Two years before, after discovering he can communicate mentally with Skye, the huge blue dragon, Jaiden had set out on a quest to help her and her family escape their enslavement by humanity. The blue dragons' first act of freedom was to make their way to Septrion, a vast desert north of the more verdent human lands of plains and mountains. However, it's a grim existence living in the desert and the dragons begin to prepare to fight for their freedom and return to their traditional lives in mountain caverns.
Skye visits Jaiden to enlist him in their cause since he had expressed earlier that he didn't want to be left out of any dragon effort to gain freedom for all dragons and not just the few who have escaped or survived the last Dragon War, years earlier. Jaiden works closely with Skye and her mate, Caerulus and is assigned to train for battle with Trigger, an escaped silver dragon who is smaller and can fly in tighter manuevers than the blue dragons. Their relationship is rather rocky because Jaiden's inexperience is viewed by Trigger as a hindrance.
Among the small community of dragons are the Founders who are much older by several decades than the Novis, the newly escaped dragons. Though the Founders had survived defeat in the Dragon Wars, they still desire to even the score with the help of the Novis. Jaiden finds the powerful Founders rather scary but equally fascinating.
Then shock spreads like a wildfire among all the dragons of Septrion when Skye and Caerulus' children are abducted by a sneak attack by humans. Jaiden and Skye make a mad dash to the nearby human town of Lynden to rescue the young dragons before they are taken to Portville, the site of the Big Barn, the main holding facility for the blue dragons who are forced to tow human-built trains. Between Jaiden and Skye's efforts, the two younger dragons are rescued but Jaiden and the older male dragon, Baldric, are taken prisoner to Portville.
Jaiden ends up in a dungeon fortress along with an old man and young woman in cells next to his. All are accused of aiding dragons and are labeled "dragon lovers." Jaiden is hesitant to share much with the other two people but slowly develops a basic trust for them. Ubel, the prison warden seems to convince Jaiden to betray the dragons and lead his band of prison guards to Lynden and attack the dragons. However, Jaiden conceives a plan to alert the dragons his is coming with a human attack force. He discovers how to communicate mentally with Baldric at a distance of a few miles and later with Skye to warn her of the coming attack.
As Ubel and his guards march into the desert, Jaiden's warning to the dragons allows them to ambush the humans and kill all of them while rescuing Jaiden and his new companions. Jaiden feels responsible for letting Baldric get taken by the humans, though Skye does not blame him. Undiscouraged, Jaiden convinces the sarcastic and reluctant Trigger to fly him straight to Portville to rescue the young dragons. On the way, he picks up three farm boys who had helped Skye and him free Caerulus and the children two years earlier.
Before Jaiden, Trigger and boys devise a way to rescue Baldric, Skye and Caerulus rush to Portville to assist in the rescue. A fierce fight with with human workers and guards in the Big Barn, near the train station, results in the boys and dragons escaping with Baldric. Back at Septrion, everyone prepares for the war to come. In gratitude, Skye gives Jaiden a crossbow, something he's always wanted and feels he will need soon.
