Jake is on out above a baseball stadium trying to stop the Huntsman from getting hold of the Uchrono Hourglass, a device capable of traveling back in time. Unfortunately, like most of his missions, he had to keep it hidden from his dad, who thought that he was still studying at the library. But after Jake finally gets a hold of the Uchrono and falls into the stadium, he ends up catching a baseball, putting him on TV. Coincidentally, the Long family was watching that exact same game.
Unable to defend himself without exposing his family's magical secret to his father, Jake was grounded for two weeks. Bummed out about being grounded for something he had to do, Susan brings Jake to the basement to show him something. She opens up an old box and pulls out an old photo album, and turns to a certain page. On this page that shows her and Jonathan at the Halley's Comet beach party on June 27, 1986. On the back of that certain page, a letter that wasn't even opened. Susan when on to explain that she was going to give Jonathan this letter on the last day of school, and explain her family being a dragon, the existence of magical creatures, everything. However, she did not give it to him, saying some secrets are better kept secret.
In the next scene, Jake heads off to the shop, to give the Uchrono to Gramps. But just learning he can use this thing to time travel with, it gave him an idea. He turns the knobs, and gets ready to use it. Fu Dog spots him, and runs over to stop him, but before you know it, both enter into June 27, 1986.
Jake explains to Fu about the letter his mom was suppose to give to his dad. All he has to do now is make sure he gets it. The two of them head off into his school, and search for younger Susan and Jonathan. Once they find him, Jake steals the letter, and shoves it in Jonathan's locker. However, from outside the school, you see Jonathan freaking out about the letter Susan addressed to him; all the way to the point where they break up. At first Jake figures this fight won't last very long, but he then realizes if he doesn't get them back together, he and his sister will not exist.
The new plan now was to get Jonathan and Susan back together. Future Jake and Fu head to the shop, to see if younger Gramps and help them in some way. Fu sends off his younger self to Atlantic City, and Jake pretends to be the Canadian Dragon named Beyonce Timberlake to prevent Lao Shi from knowing they were from the Future. However when future Fu tries to convince him that he needs to help get Susan and Jonathan back together, he laughs and cheers saying he's been waiting for the day when his daughter would dump that human.
With the current plan foiled, Fu thinks up plan B. He decides that he'll bring Jonathan to the Halley's beach party, and Jake will bring his mom. The two will meet each other there, and maybe it'll help them get back together. Unfortunately, this plan also fails when Susan heads home before Jonathan arrives at the beach.
Now with Jake, Jonathan, and Fu there on the beach, Jake decides to tell him the truth. But as any person would say they were from the future, Jonathan didn't believe him. He proofs himself with a picture he had from his pocket, and turning into a dragon. But this only terrifies him to the point of fainting.
Just as they figure things can't get any worse, they do. The younger Huntsman charges up to attack Jake. Jake puts up a fight, but the Huntsman sets off a bomb that blows Fu and him down into the sand. While they were distracted, the Huntsman steals away Jonathan's body, and takes him into a submarine.
With his dad captured, and the sand in the Uchrono Hourglass almost empty, the two head back to the shop. There, they convince Susan and Lao Shi to help them rescue Jonathan from the Huntsclan.
The four of them use an enchanted compass to find Jonathan and the Huntsclan's lair. There they sneak inside, and kick some Hunts-butt! But in a total accident, Jonathan gets hit by the falling roof, and falls down unconscious. Jake and Gramps take down the Huntsclan, and everyone gets out safely.
Back on the beach, Jonathan just starts to wake up form his injury. With this moment, Susan and Jake lie about the whole dragon situation just for his sake. With everything back to normal, the two lovers take their Halley's Comet beach party picture just as Jake and Fu head back into the future.
Back in the present time, Jonathan tells Jake that he feels bad about punishing him. He and Susan talked it over, and decided just to give him a warning this time. Jake is super excited, but starts to bum out again when his mother finds out he was time traveling from the photo her and Jonathan took on Jone's beach. Apparently, Jake was right on the side, when the picture was taken. Once again, Jake found himself grounded for two weeks without TV and video games.