went to retrieve alien gun got caught up and probed by aliens now im stuck inside space craft with sally how do i get out thanks

Reload a save before you went there or finish the entire Mothership Zeta quest line. Those are your only options. There is no way out until the end once you start it.

If you still want the alien blaster then go near the site with dogmeat and tell him to fetch a weapon, and then tell him to fetch some ammo after he brings you the gun. Just make sure to stay away from the spot where you get beamed up.

Would recommend the quest, fun and awesome loot. not only alien weapons but a epoxy for repairing your gun, very nice if you use an unique weapon like the gauss rifle or hard to find weapons like the gatling laser or the three beam. If you do it take your time and explore everything as its parts you can not get back to later.