You'll learn more in later episodes but basically Nate ran away after the whole school found out about his and Danny's affair. For someone like Nate who, along with Stacy, was part of the most popular couple, it became hard to deal with.
Nate didn't tell anyone so, instead of making it obvious he ran away, I thought i'd put a sting in the tail by making it seem he had died. When Rick's Mother (Also Nate's Mother) says "I've lost my son" she means he's actually lost!
Nate + Danny had the affair.
Rick = Nate's brother who was very close to him and blamed Danny for Nate running away.
Rick's suicide was part of delusions that Danny was having down to the guilt he felt. He had dreams which made him think Rick was actually dead and that lead Danny to his own suicide attempt.. for real.