It all came to a conclusion in the season finale of "Witches of East End." Joanna finally realized that Penelope was actually Athena, the shapeshifter who'd been targeting her and her family all season. It was nearly too late, though, as Penelope got the upper hand on her. Thankfully, Wendy showed up and the sisters were able to unite to kill Penelope.
With Penelope dead, the powers she'd stolen were returned not only to Freya, but to both of Penelope's sons, Dash and Killan. She'd revealed earlier that she stole their powers when they were little. Like Joanna's children at the beginning of the season, the boys had no idea that they ever had these abilities. The timing couldn't have been worse, as their powers came back just as Dash was confronting Killian after Freya called off their wedding. Suddenly, their confrontation got magically dangerous, to both of their surprise.
The season ended with Ingrid having just opened the portal to Asgard. She was forced to do it at gunpoint by Mike, but he was fried immediately when the portal opened. That didn't mean Ingrid was out of danger. Joanna and Wendy showed up in time to see something stepping through the portal. After all of that, Zap2It's Laurel Brown said that no one's in a good place, or, as Hollywood Life's Andy Swift put it, the whole thing was "super bananas" and "super tragic."
Thankfully, "Witches of East End" has already been renewed for a second season, so viewers will get a chance to see what new threat is stepping into the lives of the Beauchamps.
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UPDATE: A previous version of this story stated that Penelope's son was named Dax. His name is Dash.