The main girl is traveling with a boy she likes and a teacher. While they are trying to make it back home, weird things start happening such as cell signals are whack and birds are running into things. The teacher ends up getting shot and killed at a gas station, so the teens run away. One of the rogue birds cause them to wreck at area 51. The scientists use undocumented medicine to save them, but wipe their memory of it all. The girl meets a very attractive girl who she feels a supernatural pull to. This girl turns out to be an alien trying to make her remember the events that happened to her. The main girl ends up painting a mural that makes her remember.
Good chance this is Adaptation by Malinda Lo.
Reese can’t remember anything from the time between the accident and the day she woke up almost a month later. She only knows one thing: She’s different now.
Across North America, flocks of birds hurl themselves into airplanes, causing at least a dozen to crash. Thousands of people die. Fearing terrorism, the United States government grounds all flights, and millions of travelers are stranded.
Reese and her debate team partner and longtime crush David are in Arizona when it happens. Everyone knows the world will never be the same. On their drive home to San Francisco, along a stretch of empty highway at night in the middle of Nevada, a bird flies into their headlights. The car flips over. When they wake up in a military hospital, the doctor won’t tell them what happened, where they are—or how they’ve been miraculously healed.
Things become even stranger when Reese returns home. San Francisco feels like a different place with police enforcing curfew, hazmat teams collecting dead birds, and a strange presence that seems to be following her. When Reese unexpectedly collides with the beautiful Amber Gray, her search for the truth is forced in an entirely new direction—and threatens to expose a vast global conspiracy that the government has worked for decades to keep secret.
There's the birds crashing into things, traveling with the crush, the car crash and being healed, and the mysterious girl she has an attraction to. This review mentions the teacher getting shot at the gas station and makes explicit the reference to aliens.