In-game, your Alignment is a hidden value determined by your actions to create your character's "Personality", or how other NPC characters will view your character.
At the beginning of each game, your Alignment Value (let's call it "AV" for now) will be 0.
Going with a "Good" action during a quest will add +1 point to your AV, and doing a "Bad" action will subtract -1 point to your AV.
Alignment and Career are NOT the same thing, in fact they are completely unrelated apart from from a possible one-off AV point when you first join your selected Career, to make up for how NPCs will see the organisation your character is part of. The only Careers affected by this are the Seeker and Gang Member - with when joining the Seekers you will receive +1 AV Point and if you go down the Gang Member route you will lose -1 AV Point. The Researcher and ordinary Trainer Careers will not give any AV Points, nor do the Side-Careers of Breeder and Gym Leader.
-15 - -5
-5 - 5
5 - 15