Alex harbours a longtime crush on Isabel, and Isabel feels something too, but is scared to let anyone in because of her secret and the risks it involves. She and Alex teeter on the brink of something several times their sophomore year, but Isabel remains reluctant. Eventually, once Alex knows about the aliens, Isabel says she can't handle a true romance with him, while being hunted by the FBI and learning about her background. Alex agrees to be a friend and support in Isabel's life and she dates other people their junior year, though never anything serious. Eventually Isabel lets herself open up to Alex and they go to the prom with the intention of finally starting a real relationship. Days after the prom, Alex is tragically murdered by Tess and Isabel is beyond heartbroken, feeling there is no reason left for her to stay in Roswell.
Though Alex has noticed and has a crush on Isabel, they don't really know each other, but Alex tries to get to know Isabel and opportunities present themselves once Maria and Liz know Michael, Max and Isabel's secret.