This level should be the last adventure (or misadventure) for Linkle. It is also perhaps the only time you see a cutscene of Midna turning into Twili Midna. If you need your memory jogged, play Twilight Princess to the end credits to see Midna's true form. This stage takes place after Link got a hold of the Master Sword, with everyone preparing to attack Cia's army at the Valley of Seers.
Open those bases!
Zelda is currently worried about the dark magic in this place and is trying to keep Dark Twili Midna from spreading her powers around. What's worse, Dark Zant is blocking the Enemy Base. Take the bases on the left before joining up with Twili Midna on the middle southwest. Take the bases on both middle south and northwest.
Dark Zant on fire
For the time being, Dark Zant is fired up and can kill you instantly, so avoid him for now. Run as fast as you can and take the remaining bases around the corners and also protect the Allied Bases. Doing so will make Zant's powers weak enough to defeat him.
If you've done all of this quick enough, get Twili Midna to open the last door for one final fight. If Zelda's health is too low, hurry to her and she'll heal automatically. Now aim for Dark Twili Midna and take her down to end this level. In a cutscene, Twili Midna will take responsibility since she owns the place. Linkle and Zelda will leave and after Twili Midna breaks the source power, she'll turn back into a magical flying imp that you have seen before.
Will Linkle make it in time? Hyrule Castle might've already changed so be ready for Linkle's final level.