Lunar's alive!!! and somepony kept it secret. When Scootaloo finds out who's been hiding in the Cutie Mark Crusader Tree house, she just can't keep it a secret.
And it seems somepony has been spending an unusual amout of time without her friends recently.

2nd Story of 'Lunar's Misadventure'

1st story: http://www.fimfiction.net/story/24222/The-Start-of-Something

Possible to read without the first but I wouldn't recommend it…
(Note: 3 of Mane 6 to be introduced later)