Haynes left the series after the second season to work on Arrow.
Scott is blackmailed into helping Gerard Argent after the latter threatens Melissa's life by becoming a mole in Derek's Pack.
His and Allison's romance then becomes strained due to their conflicting loyalties and then by Allison's increasingly violent behaviour because of Gerard's manipulation of Victoria's suicide.
Scott later learns his father, Rafael is back in town something he and Melissa aren't too happy with, as he'd left the family when Scott was only a toddler.
In Season 3B, because of his Druid sacrifice, Scott now carries the burden of having a darkness around his heart like a scar.
This causes him fear of shifting into his new Alpha form.