Before you jump the gun, Linkle is unrelated to Link. Linkle is a girl who carries two crossbows. She does wear a green tunic but she also has a special compass from her grandmother with the Triforce symbol on it. Although Linkle never meets Link in her adventures, she'll go on her own misadventure as she misinterprets her map. Also, if you're expecting soldiers as her allies, instead (at least in all Linkle's levels) her allies is nothing but Cuckoos! Yes, not only that, brown and gold cuckoos will be there as a sidequest, provided that you know how to protect it from monsters and ghosts!
Majora's Mask wants to play
Veterans should recognize that this mask and its wearer, the Skull Kid, play a major role directly after Ocarina of Time. Young Link must reset time over and over again with his ocarina (and a few other instruments in Goron, Zora, or Deku form) to end the crazy cycle of getting that mask back. Here, with Tatl and Tael, the Skull Kid steals Linkle's compass and she is forced to chase him around the woods. The middle area and the southeast corner will be available at the start.
Base after base after base
This level is pretty forgiving. Go to where the Skull Kid is as he'll disappear and reappear on a different base. If you take too long, he'll summon a few monsters to track you and take you down. Since most of the bases are closed, you'll have to track down the Skull Kid to open them. He'll start on the top middle base, where you have to take the gate keeper down.
He'll teleport to one of the bases on either the middle-south or the middle-west. At the same time, there will be Gibdos or any other monster attacking your Allied Base. Make sure your Allied Based is no longer in danger. He'll also eventually open up the Fairy Fountain and the northwest corner. This is the time to take the Skull Kid down, or delay a little a longer to let the last southwest corner base be opened.
Linkle fights back
As long as you overtake all available bases, the Skull Kid will have no place to summon or control the monsters, so attack him as much as you can. In the midst of it, your compass shines a blinding light, giving you a chance to end his mischief once and for all. He promises not to do it again if he can steal something else?! The Skull Kid will never learn.
Linkle will continue on her adventure, if she's going the right way. The cutscene will explain her background and what drives Linkle to become a hero.