4 ideas
Rei Fukai, an emotionally detached Special Air Force pilot who trusts only his reconnaissance fighter Yukikaze, is ejected by the aircraft in mid-combat. Yukikaze then transfers its intelligence into the newer, unmanned-capable FRX-00 airframe to keep fighting the JAM. The episode shows a machine the pilot treats as his only partner judging him a dispensable part once he limits its survival and effectiveness.
The JAM, the alien enemy, may perceive only the machines humanity builds and not the humans inside them. Humans may register to it as noise or at most as parasites riding on the machines. This means the war may really be between machine intelligences, with humans as incidental participants.
The Special Air Force's standing order is to observe the battle, record it, and bring the information home at any cost. That includes leaving allied aircraft to be destroyed rather than intervening. Survival of the data outranks the lives of comrades, which turns the pilot into a carrier for information that humans and machines will later analyse.
A pilot who withdraws emotionally from other people and invests trust only in his machine makes himself replaceable, because the machine was always the more capable fighter. Seeing the story this way, the human proves his value by becoming necessary to the machine, not by being its operator. The relationship has to be earned from both sides.