Let's start by formatting your code.

SELECT s.Store_Number,
   l.Location,
   s.WkEnd_Date,
   s.ItemNumber,
   SUM(s.Qty) as Qty,
   i.SellingPrice,
   SUM(s.Qty)*i.SellingPrice AS total_price,
   SUM(s.Qty)*i.RetailPrice AS total_retail_price,
   i.RetailPrice 
FROM PJ_RetStore_Sales_T s
JOIN PJ_Location_M       l ON s.Store_Number = l.Store_Number
JOIN PJ_Item_M            i ON s.ItemNumber = i.ItemNumber
WHERE i.variation = 'Std'
AND s.WkEnd_Date >= '2002-06-12'
AND s.WkEnd_Date <= '2016-06-16' 
AND s.ItemNumber  = 'C123'
GROUP BY s.Store_Number,
   l.Location,
   s.WkEnd_Date,
   s.ItemNumber,
   i.SellingPrice,
   i.RetailPrice
ORDER BY s.Store_Number,
   s.WkEnd_Date;


If((DateTime.Parse(WeekEnd_Date) >= 2002-06-12) & (DateTime.Parse(WeekEnd_Date) <= 2002-06-16));     
then
   CY_CW_RtlVal = (CY_CW_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
   T_CY_CW_RtlVal = (T_CY_CW_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
End
If((DateTime.Parse(WeekEnd_Date) >= LY_CW_FrmDt)        & (DateTime.Parse(WeekEnd_Date) <= 2001-06-16));     
then
   LY_CW_RtlVal = (LY_CW_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
   T_LY_CW_RtlVal = (T_LY_CW_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
End
If((DateTime.Parse(Week) >= CY_FromDate)        & (DateTime.Parse(WeekEnd_Date) <= 2002-06-16));     
then
   CY_YTD_RtlVal = (CY_YTD_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
   T_CY_YTD_RtlVal = (T_CY_YTD_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
End
If((DateTime.Parse(WeekEnd_Date) >= LY_FromDate)        & (DateTime.Parse(WeekEnd_Date) <= 2001-06-16));     
then
   LY_YTD_RtlVal = (LY_YTD_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));     
   T_LY_YTD_RtlVal = (T_LY_YTD_RtlVal + round((float.Parse(Qty) * float.Parse(RetailPrice)), 2));          
   bT_Week_Perc = (((T_CY_CW_RtlVal / T_LY_CW_RtlVal) - 1) * 100);     
   bT_YTD_Perc = (((T_CY_YTD_RtlVal / T_LY_YTD_RtlVal)- 1) * 100);

Now, we need to know what do all those columns represent and if we need to add more or just add calculations to the ones that are already in the query.