Is it true that when God permitted the spirit of Samuel to be witnessed by King Saul and his son Jonathan, it signaled a change of course for Israel’s history forever?
To answer this question we need to look at the entire chapter of 1 Samuel 28. The chapter never mentions his son Jonathan. So I don’t know where you are getting the idea that they were together. King Saul goes on his own with two of his servants. His son Jonathan is a prince, not a servant.
Saul was afraid of the Philistines when he saw their army in full array (1 Samuel 28:4-5). The kings of Israel always consulted the Lord to find out whether they would win the battles or not. But because God’s Spirit was no longer leading Saul, he heard nothing from the Lord (1 Samuel 28:6).
King Saul had been making the wrong decisions for a while now without the Spirit leading him and God’s blessing on his life. God had already chosen and anointed David as the next king of Israel. So he was no longer speaking to Saul. If Saul would have been godly, he would not have followed the next steps.
He immediately turns to his servants and looks for an alternate spiritual source, a sorcerer or necromancer (1 Samuel 28:7-8). This is a person who has the ability to see into the spiritual world and pull up the spirits of the dead.
If the Bible speaks of it in this way, this is a real and dangerous thing. Mosaic law forbade raising spirits from the dead and speaking to them. It also forbade sorcery and witchcraft. So everything that happened from this point violates God’s law in the most extreme way. God must be our spiritual source of truth.
Saul’s servants are very helpful because they know of this woman, this sorceress, right away. Apparently, his orders carry little weight because he banned all sorcery from the land of Israel. It was way too easy to find.
Again, Saul should’ve stopped here. Instead, he disguises himself so no one will know that the king who banned sorcery is now seeking it as his only spiritual source for information (1 Samuel 28:8). This sorceress listens to what he wants to do. But she is worried about getting caught.
Of course, he names Samuel. Now Samuel had died most recently and was buried in his own city (1 Samuel 28:3). The way the Scriptures talk about this, it was a most recent death. There is a belief among the Jews that a soul is available for three days after death to be resurrected (This is why Jesus waits for four days to go see Lazarus, so the Jews did not think he resurrected Lazarus because he was yet to transfer to Sheol).
The woman refuses to do this for him because it is banned in the land and she does not want to be killed by King Saul who ordered it (1 Samuel 28:9). Saul assures her that no harm will come to her (1 Samuel 28:10).
She agrees to do what he asks, to call up Samuel from the grave. It is this woman who sees Samuel and realizes she is speaking to the king (1 Samuel 28:11-12). He tells her to call up Samuel.
Then she sees Samuel the prophet. She may have known what he looked like. And if not, the description she gives of an old man wrapped up in a robe may speak to the prophetic mantle (1 Samuel 28:14). Her description is a dead giveaway for the King.
There is no indication that neither the woman nor Saul don’t believe that this is Samuel’s spirit. In fact, both take it to be true that they are speaking to Samuel. There is no deception in the language here. When Scripture is so straightforward, there’s no need to challenge it.
Saul asks Samuel to give him guidance for the battle at hand and Samuel asks why he has disturbed him (1 Samuel 28:15). Samuel tells them that the Lord has rejected him and asks why he would turn to another source like himself (1 Samuel 28:16-18). Samuel reminds Saul of his fate because he did not listen to the Lord.
Then Samuel proceeds to tell Saul that because of his turning away from the Lord, he and Israel will be defeated in battle. Worse than that, he and his sons will die in the battle the next day (1 Samuel 28:19).
Saul takes Samuel’s words for the gospel truth. He believes and when he says that he and his sons will die the next day (1 Samuel 28:20). So there is no question in Scripture that this is an accurate account and description of what Saul did.
We find out later in 1 Samuel 31 that everything happens as the prophet Samuel said. Just as he could predict the future as part of his prophetic gift from the Lord in his life, he also could do so in death.
Israel’s history was already on a different course from Saul. The moment God’s Spirit left him and God anointed David as the next king after Saul’s death, Israel’s history was on a different trajectory. Saul’s end is a sad account of what happens when we disobey the Lord and do our own thing.
As far as the spiritual nature of this account in 1 Samuel 28, the spiritual realm is a real place where these kinds of things can happen. We need to be aware of it, but not dwell on what the Bible reveals about the spiritual realm. There are reasons why God tells us not to do certain things.
Whether God was the one who allowed Samuel’s spirit to come up and speak to Saul or there was another force at work through evil spiritual forces that this sorceress could control, we don’t know for sure. But it is best to be on God’s side in spiritual matters.