Pre-Series
Applejack was born amongst the extended Apple Family. While not much is known of her particular past as of yet, it is implied that she had to grow up without her parents. How they were lost is unknown, but it made Applejack a lot more self-reliant and mature, as she had to take care of things where her parents had to before her.
As a filly, Applejack moved out of Sweet Apple Acres to live with her upper-class relatives, the Oranges over in Manehattan. She soon began to find that it was very hard to fit into city life, and eventually became very homesick. The rainbow left in the wake of Rainbow Dash's Sonic Rainboom convinced her that being in the family farm was where she truly belonged, and this earned her her Cutie Mark.
Season 1
As the Plunder Vines were infesting Ponyville, Applejack went off to find the Tree of Harmony, having Twilight Sparkle staying off behind as she agreed it to be the best decision. During her attempts to get to the tree, she and the others end up found by the vines, and she tried to fight it off, only to be dragged to Earth, waking up by Rose Fountain. She went with the others around Beach City until Discord brought them all back home.
During a harvest sometime later back at Sweet Apple Acres with Apple Bloom and Big Macintosh, she heard word of the Poison Joke affecting the others thanks to a visit from Steven Universe, Amethyst, and Lapis Lazuli, recognizing it as Poison Joke rather quickly after seeing Amethyst, claiming they only grow in Everfree Forest, before directing them to Twilight's Library.
Season 2
Applejack's role in Season 2 is mostly a side character role: aiding in building the Galactic Ray, and aiding the Gems once they got to Homeworld.
Season 3
When she got word of her Great Granduncle Chili Pepper's sudden departure from Canter Creek, she went there as the town looked to her to help settle things while he was away. She introduced them to Chili Pepper's ranch, and Tumbleweed. When Longhorn arrived, and whacked Tumbleweed aside, Applejack was the first to step up to the outlaw, but got knocked back hard before she could land any blows. She went out later that night to track them down, only to find her relative's barn up in flames, and finding a warning from Longhorn to get out of town. The next morning, she and the others built a "Syrup and Feather trap", which didn't work, and she only got even more upset when she found him trying to get a more legal loophole, and sign the ranch to him. Finding all this out, she made up her own plan; move their campsite off the property and distract Longhorn with extra documentations, biding them just enough time to have the ranch deemed a historical site, and as such, unable to be signed off to Longhorn.
During the involvement with the Time Jumper, she and the other ponies were teleported to the future.
Season 4
When Twilight discovered an Equestrian Coelacanth, she went with her along with the others in order to help track her down, only to end up lost out in the sea. She reassured Twilight that it wasn't her fault, as she never knew it would happen, prior to finding their way to the Blue Diamond Ruins, discovering that Warp Pads were built on Equestria.
Applejack and the others got word later from Connie II about her imprisonment by Starlight Glimmer, and she and the others went off in order to find her at the location. Applejack began to question the town, especially after meeting Starlight herself, and got to the point in order to find her, only to get nothing. Applejack went off on her own at one point, and avoided getting captured by the time she came back to the others, just to find Connie II in town after all. Ticked off at being lied to, she got Connie II free, and in the end had to wait. This didn't last too long though, and she went off with Connie II to retrieve the missing Cutie Marks. Starlight though caught her, and tried to remove her mark. AJ had her distracted so Connie II could get the marks out, and lead her back into her town, having her blast open the cell to the rest of her friends. She got her Cutie Mark taken after this. After realizing she ran for it, Applejack went after Starlight and she managed to get Rarity and Pinkie's Cutie Marks during the chase, and helped in getting the rest back altogether.
When Sapphire was taken, she was amongst those used as a offering for the Human Zoo. She had to wait it out in there as well until team B of the Crystal Gems arrived and got them all out.
Season 5
Cluster Arc
As Amethyst and Steven were off on their monster hunting mission, Applejack and the others decided to lend a helping hoof with them, in particular with the Gem Tortoise and Tongue Monster at the Beta Kindergarten. She in particular went with Steven and Amethyst after the Gem Tortoise. During her monster hunting, she and the others came across Blue Diamond, and she in particular sympathized with her, telling her about her own loss in her family, showing Blue Diamond other beings understood her, and that it was a feeling hard to be okay with.
Before she could return to the others about the Cluster, she found out about Malachite, and went with the others to regain her. She helped get Lapis Lazuli and Jasper back to the Barn House before going off to confront the other Gems about the Cluster.
Serpent Arc
After getting her cider together for Beach City, she and Rainbow Dash discovered the involvement of the Restaurant Wars, and both decide to put an end to the argument. She tried multiple ideas, with most of them sabotaged by Acid and Cyanide. On the final attempt, she herself caught them and tied them both together so they wouldn't intervene, but she lost them shortly afterwards.
Season 6
During one typical work day at Sweet Apple Acres, she got Jasper, Lapis, and Peridot to help out as cider season was right around the corner, when she got a letter from Paula Red. She went off to White Tail Woods in order to build the house for Connie II, and later on helped make the house a home for her when she arrived.
As she got ready for the Apple Family Reunion, she began to take some note on Steven Universe's predicament, as this happened after Connie had left him. She helped him out, telling him he should take his mind off of it for a bit and that it might not be as bad as he was thinking. Throughout the reunion, Applejack tried to cheer Steven up, but with little success.
After some time though, like everyone else with the exception of Spike and the Rutile Twins, ended up captured by White Diamond, and unable to leave until after the humans arrived to save them.
She makes an appearance in the alternate universe within "Butterfly Wings". In this alternate world, Twilight Sparkle and Spike arrive to try and get some answers, only to have her not recognize her, Pinkie Pie, or Rainbow Dash. She was able to recognize Rarity, but saying that she had moved to Manehattan to help with the war between the Crystal Empire and the Lunar Empire. She didn't believe them at first, but after a while suggested that they go to see Nightmare Moon, hoping their involvement would fix everything.