In this chapter, the LORD speaks to young Samuel and Samuel begins ministering prophetically.
The first thing I would like to point out is a very subtle thing that many readers might not otherwise notice, which is in verse 3. Do you see it? "And the lamp of God had not yet gone out." What is the lamp of God? It is the lampstand that is contained within the tabernacle, opposite of the table of bread of the presence (also known as the table of showbread). From this verse, we can infer that it was an ordinary occurrence for the lamp of God to eventually burn out, because the word "yet" implies that it was something that happened often; perhaps every night.
The author only mentions it to give us an idea of what time it is, but there is a subtle implication: the priests are not doing their jobs. The priests were commanded to keep the lamp of God burning continually for all their generations (you can read about this command in various places: Ex 27:20, Lev 24:2) In my opinion, this is the author making a sort of passive-aggressive criticism of Eli and his sons for failing in their duties. Incidentally, this is another case where the author is not explicitly condemning Eli's actions, but we should be able to read what is going on. Not only are Eli's sons disregarding the Law by eating fat and committing sexual immorality, they are also disregarding their duty to maintain the tabernacle in such things as the golden lampstand. This is just one more thing to show us the kind of society that existed at the time and how the people and priests related to the LORD. There were definitely righteous men and women, such as Hannah, who obeyed the commandments of the Law, but then there were other people who did "what was right in their own eyes" such as Eli's sons.
The second part of verse 3 is also interesting. It shows that Samuel was sleeping in the tabernacle "where the ark of God was". It's worth mentioning that this verse actually uses the word "temple" instead of "tabernacle", which in this case is an anachronism because the temple hasn't been constructed yet. This is why I haven't talked about the temple at all, because it was not described in the Pentateuch. Just so my readers understand, the temple is essentially the exact same thing as the tabernacle in both purpose and design; however, the temple was built as a permanent construction, while the tabernacle is designed to be taken down and set up so that it could travel with the Israelites through their wandering in the desert. The first reference to the "temple" was in 1 Samuel 1:9, and this is the second such reference. In my opinion, this subtle change in language indicates that Samuel (and subsequent books) were probably written by a different author or in a different time than the earlier books of the OT.
But that wasn't the thing I wanted to point out. What I wanted to point out is that Samuel is sleeping near the ark of God, which would have been in the most holy place that should have only been visited by the high priest once a year. This verse is implying that either the ark was not kept in the most holy place, or that Samuel was permitted to sleep in a place that should not have been visited by Levites, much less by an Ephraimite such as himself.
What makes this even more striking is that the LORD doesn't rebuke Samuel for what he's doing; in fact, the LORD takes this as an opportunity to speak to Samuel and favors him. By all appearances, Samuel is also violating the Law, just as Eli's sons violate the Law. However, Samuel is favored for his actions, while the LORD (in the previous chapter) condemns Eli's sons to death. What is the difference between Eli's sons and Samuel? I believe the answer is honor. Samuel desired to honor the LORD, and slept in the presence of the ark because he desired to be closer to the LORD. Eli's sons sought to enrich themselves and take advantage of their power for personal gain. I think this is an important example of how the LORD is not seeking strict obedience to the Law, but obedience to the spirit and intent of what the Law means. It is primarily expressed in the Shema of Deut 6: To "love the LORD your God with all your heart and with all your soul and with all your might."
We don't know Samuel's story, but in whatever way, he has earned the LORD's favor. The LORD calls him three times, but for some reason he thought it was Eli calling. Perhaps he heard the LORD's voice out loud and mistook it for Eli? Eli is also slow to figure out that it is the LORD calling him, and Eli seems to share Samuel's confusion. V. 10 is another interesting verse, because it says the LORD "came and stood... as at other times". This suggests that the LORD not only spoke to Samuel, but was in some way present in the tabernacle where Samuel was sleeping.
The particular message that the LORD shared with Samuel is almost the same as what we read in the previous chapter. It's pretty strange to imagine Samuel as a young child prophesying destruction to the high priest Eli, an elder, one of the chief leaders of Israel.
In the end, "the LORD appeared again at Shiloh" because of the prophecies of Samuel. This draws a sharp contrast against v. 1 when "word from the LORD was rare in those days". Eli and his sons did not honor the LORD, so the LORD did not honor them by sharing "words" with them. With Samuel, all of Israel knew that he was a prophet because the LORD spoke to him and fulfilled the words that he spoke. It appears that Samuel's faithfulness is helping to restore the word of the LORD to the entire nation, although the unfaithful priests have yet to be dealt with.
In the larger context of Israel's history, we can see how the delinquent priesthood plays along with Israel's anarchy. The people do "what is right in their own eyes", and the priests seem to behave likewise. There have been a handful of righteous men and women, sometimes the judges and sometimes ordinary folk like Hannah or Jael, but the culture at large has been rebellious and sinful. Samuel's rise as a prophet is similar to the judges who came before him (such as Deborah, who was known as a prophetess), but as we will see from the length of his account, Samuel will play a far more transformative role. The earlier judges "saved Israel from their enemies", but Samuel will help bring a more profound transformation to the nation from the inside out.