Alison is the only one that can get through to Beth, she's the only one to keep her steady and strong. Beth is the de facto leader of their little Clone Club and they all expect her to have it all sorted, to keep it together for everyone. But Beth is just as vulnerable as the others, she can't always shoulder everything. It's in the quiet and darkened early hours of the morning when the burdens raise their ugly heads in Beth and it all becomes too much to cope with. Alison is always there though to hold her while she lets it all out.
In the dead of night all of Beth's fears and worries bleed out of her and Alison puts her back together piece by piece as best she can. In the stark light of day Beth's mask is back on again, strong and steady, the cop. The leader. The cracks then are less noticeable, a nervous tick here, a slightly too heavy sigh there. Mostly going unnoticed by her partner and Paul, even Cosima on her occasional visits from Minnesota. Alison always notices though. As a woman who spends her whole life working to a meticulously planned schedule, little escapes Alison, especially when it comes to Beth.
Alison knows there isn't much she can do for Beth as she fights her way through her demons. But she can be there for her, hold her when the nightmares are at their worst, soother her frantic three am phone calls when she's paranoid and worrying and can't sleep. And Alison succeeds where Paul always, always failed, she can break in past that mask and stony front. She both hates and appreciates Paul for all his failures at the same time. On the one hand he should have cared more about Beth, he should have felt that same drive and desire to take care of her and keep her safe. To love her. Beth deserved better than him. On the other hand, without Paul all of those things fell to Alison instead, and for that alone she was grateful to Paul and his shortcomings as both lover and monitor.
In the end it always comes down to just the two of them, both wrapped up in this mystery that is steadily driving them both insane. The worse Beth gets, the more Alison worries, the more pills Beth takes, the more Alison drinks. They know they're both losing their grasp on their realities, their families and jobs, but it doesn't seem to matter quite so much when they're together. Alison knows that this isn't normal, this thing they have. But after all that she's seen since Beth first called her all those months ago and mentioned the C word, she's lost the ability to care anymore.
Alison is the only one can get through to Beth. She's the only one keeping Beth from flying off the rails, and while she'd never admit it, she knows that Beth is in some way keeping her from losing it too. They might not be conventional or normal in any sense but hell, they're clones. There was never anything natural about them to begin with. Despite it all, they work.