Kanata no Tokei

Main character attends a school where students are in average 17 years old, but who have to repeat school year due to an accident. He usually goes to school with younger sister who is a heavy sleeper and always wants to sleep more in the mornings by saying "I want to stop time". And mysterious watch controlling time gets found. When secret wishes of people are met the watch starts to shine.

"I want to protect dear people"
"I want to overcome my fears"
"I want to atone for my sins"

[From vndbreview]