If she wants to have the company of the child, she has to file custody case. But as the boy was living for a pretty long time with the father, it would be difficult for her to get custody. As the boy is about 13 years, the court will ask the boy about his preference - with whom he wants to live. His choice will be very important for the court to decide the issue. Do not feel disheartened. The court will give visitation rights to the mother. For some days, the boy will be allowed to stay with the mother. Coming to the reconciliation - yes, she can attempt for that, by filing Restitution of Conjugal Rights case (It should be dealt deftly so that no harm would be caused to the lady) and this case starts with mediation and there she can put her best efforts to reconcile. If he does not agree for this, then she has to withdraw this case otherwise, husband may get benefit of this case by filing divorce.
Wish her best luck.