Homebound Odyssey: The Foundation by J. Hamilton

In the distant future, humanity is spread thinly across the universe after Earth is destroyed by nuclear chaos. In a last ditch effort to defeat the invaders known as the Drought, the military now relies heavily on the use of highly skilled task force agents that have been trained in combat since childhood.
The training spaceship, The Homebound 11, has a reputation for producing some of the greatest soldiers in Earth's history, and Garrett and Skylar are preparing to follow suit. As they both strive to show their worth, the ship's mysteries begin to unveil themselves. While fighting to overcome the issues they face within, a dangerous outside force sets them both on the beginning of a perilous journey they never would've imagined.