One day, I decided to travel without him and told him to go back to the Luck 38 and he did. I wanted to do his side quest so i tried to take him on my travels again, so I told Raul, my current humanoid companion, to go to the Lucky 38. But when I talk to Gannon, it doesn't have the dialogue option of him travelling with me. I checked the others and they can travel along. What happened? Can i get him back so i can do his side quest?

If you have E-DE with you, fire him for a while (as in, send him off to the Lucky 38, so you don't lose track of him), then talk to Arcade. The option for him to travel with you should be back. Then you can rehire E-DE as well.

Guess Arcade really doesn't like E-DE, huh.

If you don't have E-DE... sorry, don't know.