Affleck and Shookus dated for over a year following his split from Garner, his wife of 10 years with whom he shares three children -- 12-year-old daughter, Violet, 9-year-old daughter, Seraphina and 6-year-old son, Samuel.
Garner was photographed arriving at Affleck's house on Wednesday looking visibly upset outside his Pacific Palisades home.
"Garner was very emotional but decided to take the situation into her own hands," an eyewitness tells ET. Garner appeared visibly shaken. "She looked distraught."
Later, Garner and Affleck, along with the actress' bodyguard, were seen driving away from Affleck's house with the Argo director sitting in the backseat, looking distressed.
Garner was also spotted handing Affleck a bag of fast food before the car arrived at what appeared to be an L.A. area rehab facility.
On Wednesday, a separate source told ET that the Justice League star has "worked very hard to stay clean" since his last stint in treatment, but there are concerns that he could be backsliding.
"Jen [Garner] is proud of the strides he's made, but some of his friends were worried he might be taking some steps backward and could be on a slippery slope," the source said."Ben wants nothing more than to get sober for his kids, for Jen and also for his career."
The source added that Affleck "realizes the dangers of what he could lose in life if he doesn't stick to the program, and dedicate himself to these big changes."
"Sadly, he also seemed to be putting himself in some unhealthy situations for someone who has plans to sustain a sober life," the source continued. "Ben was back to staying out late and hanging with his old crowd."
"Just the other night he was out late with a group of old friends and lots of women, all who were partying up a storm," the source said. "It's truly worrisome for those who have seen him fall off the wagon in the past. The bottom line is he was going out again and hanging with drinkers, and it seems to have all happened too quickly."
The source also said that his romance with Shookus was a healthy, positive and supportive relationship that kept him on his sobriety path. But things went south after their relationship came to an end.
"Lindsay was a huge support to Ben and he was doing really well. She truly helped him with his sobriety and Jen loved that he had a steady situation," the source said. "Lindsay thought they had a future together, and she was a positive influence on him, but he felt tied down."
ET has reached out to Affleck and Garner's reps for comment.
In a heartfelt statement on Facebook, the actor said he wanted to be "the best father I can be" to his children, and praised his ex, "Who has supported me and cared for our kids as I've done the work I set out to do."
"I want my kids to know there is no shame in getting help when you need it, and to be a source of strength for anyone out there who needs help but is afraid to take the first step," Affleck wrote at the time.