I would remove the remnants of the old pigment with a wood cleaner such as Defy. Let the wood dry for two days and then apply two coats of a quality stain about 45 minutes apart.
If this is cedar also use a brigtener after cleaning.
I see you are in Mich. This winter was very hard on my decks. I've even lost pigment on some areas. Since we had zero snow to act as a protective covering, we had all that extra sun damage. This week was perfect weather to work on them too, but I really wasn't thinking about it and realized it too late. This coming week looks to be excellent weather for deck work too.