In "If I Can't Write My Chocolate Song, I'm Going To Take A Nap" Berta, refuses to keep house for both Alan and Jake, and she quits. Alan takes over as Charlie's new housekeeper, but he does a job far worse than Berta used to. Alan is tired of Charlie's misbehavior and tries to make peace with Berta by finding her and attempting to bring her back.
In "Castrating Sheep In Montana", Berta discovers that Alan has been dating her daughter Naomi, but welcomes him into the family—which would be great except Alan wants to stop dating Naomi, but doesn't want to break his new relationship with Berta. At diner which includes Alan, Naomi, Charlie, Jake, Berta and Evelyn, Naomi's ex-boyfriend Hector, comes over and they [Naomi and Hector] get back together, and Alan gives them his blessing.
In "People Who Love Peepholes", when Alan is prepared to leave the beach house, Berta asks for a hug goodbye, saying 'despite everything, you and I were like family'. But ending with 'I'm taking your room, zippy'.
In "The War Against Gingivitis", Alan gets upset that Walden never thanked him for bringing him [Walden] back together with Billy. So Alan goes over to Berta's house, calling her his 'friend'. Berta sends Alan to give a guy money, saying 'most' of it was in there.
In "Give Santa a Tail-Hole", Alan begins to feel alone and miserable, until a less-than-willing Berta comes to seemingly comfort him.