I still thinking and news ideas comes in my mind. What if there is two aliens (or half one). Like Jessica said the alien who escape have a daughter, humain one certainly but with some blood aliens too, the alien told her about Roswell and the crash, about the pod and when she is adult she come back at Roswell. either she find in love with daddy Manes coincidently and find what he done later or she already know. At a moment, Jim Valenti break his partnerships with Daddy Manes because he find the truth about the aliens : peacful Mommy Manes and the pods, she gave him the alien part of the tech she had (his mother gave her before) and explain everything to him. He choose to help them because she is a nice person and it’s why he helped Alex by give him the cabin, because he is a half alien too and a nice boy like his mom.
Part two there is a second alien, a real one, who is very bad, maybe the grand fathers of Valenti and Manes keep him alive and prison, have done something to him, implant or i dont know what and he works for Daddy Manes now. He or she is more powerful than the pod squad and can take control of mind. Manes obliges to kill every person who know too much by taking control of a bodies like Isobel and Wyatt. Manes want the project be secret, protect earth, Manes strength the alien to kill Jim Valenti because he know too much, same for Grant and try to Liz. For Rosa, maybe he have autorisation (or not) to take bodies and find «*in love*» with Rosa and tell her he is an alien and after we know what coming her.

and insighful