Get this stuff into the repo before I mess with it

scenes/analyzers.tscn

-[gd_scene load_steps=2 format=3 uid="uid://fe1lihrecu3u"]
+[gd_scene load_steps=3 format=3 uid="uid://fe1lihrecu3u"]
 
 [ext_resource type="Script" path="res://scripts/Analyzers/analyzers.gd" id="1_u0rar"]
+[ext_resource type="Script" path="res://scripts/Analyzers/level_1.gd" id="2_masw0"]
 
 [node name="Analyzers" type="Node"]
 script = ExtResource("1_u0rar")
 
 [node name="Level 1" type="Node" parent="."]
+script = ExtResource("2_masw0")
 
-[node name="Timer" type="Timer" parent="."]
+[node name="Timer" type="Timer" parent="Level 1"]
+
+[connection signal="timeout" from="Level 1/Timer" to="Level 1" method="_on_timer_timeout"]

scenes/main.tscn

-[gd_scene load_steps=6 format=3 uid="uid://daggped4nujna"]
+[gd_scene load_steps=7 format=3 uid="uid://daggped4nujna"]
 
 [ext_resource type="Script" path="res://scripts/Main Interface.gd" id="1_ltn0e"]
 [ext_resource type="PackedScene" uid="uid://bc2qthu8tugim" path="res://scenes/click_target.tscn" id="2_2hdm6"]
 [ext_resource type="PackedScene" uid="uid://c4ocioaw64kq2" path="res://scenes/messages.tscn" id="2_d66gc"]
 [ext_resource type="PackedScene" uid="uid://b6w7cs7fffyv7" path="res://scenes/generators.tscn" id="3_qm46o"]
 [ext_resource type="PackedScene" uid="uid://fe1lihrecu3u" path="res://scenes/analyzers.tscn" id="4_kptdw"]
+[ext_resource type="Script" path="res://scripts/flag_keeper.gd" id="6_1or7f"]
 
 [node name="Main" type="Node2D"]
 
 
 [node name="ClickTarget" parent="Main Interface" instance=ExtResource("2_2hdm6")]
 
+[node name="Flag Keeper" type="Node" parent="Main Interface"]
+script = ExtResource("6_1or7f")
+
 [connection signal="narration_end_introduction" from="Messages" to="Main Interface" method="_on_messages_narration_end_introduction"]
 [connection signal="end_introduction" from="Messages/Narration" to="Main Interface" method="_on_narration_end_introduction"]
 [connection signal="gl1_click" from="Generators/Level 1" to="Messages/Score" method="_on_level_1_gl_1_click"]

scripts/Analyzers/analyzers.gd

 extends Node
 
 @onready var l1 = $"Level 1"
-@onready var timer = $Timer
+@onready var timer = $"Level 1/Timer"
 
 
 # Called when the node enters the scene tree for the first time.

scripts/Analyzers/level_1.gd

+extends Node
+
+@onready var timer = $Timer
+
+# Called when the node enters the scene tree for the first time.
+func _ready():
+	pass # Replace with function body.
+
+
+# Called every frame. 'delta' is the elapsed time since the previous frame.
+func _process(delta):
+	pass
+
+
+func _on_timer_timeout():
+	pass # Replace with function body.

scripts/ClickTarget/buy_l1_analyzer.gd

 extends Button
 
-@export var cost_per_tick: int = -1
+@onready var main_interface = $"../.."
+
 
 # Called when the node enters the scene tree for the first time.
 func _ready():
 
 # Called every frame. 'delta' is the elapsed time since the previous frame.
 func _process(delta):
-	pass
+	text = "Add L1 Analyzer (costs " + str(main_interface.l1_generator_purchase_cost) + ")"
 

scripts/ClickTarget/buy_l1_generator.gd

 extends Button
 
-@export var current_cost = 10
+@onready var main_interface = $"../.."
 
 # Called when the node enters the scene tree for the first time.
 func _ready():
 
 # Called every frame. 'delta' is the elapsed time since the previous frame.
 func _process(delta):
-	pass
+	text = "Add L1 Generator (costs " + str(main_interface.l1_generator_purchase_cost) + ")"
 

scripts/ClickTarget/energy_creator.gd

 
 # Called when the node enters the scene tree for the first time.
 func _ready():
-	pressed.connect($"../..::_on_energy_creator_pressed".bind(energy_created))
+	pass
 
 # Called every frame. 'delta' is the elapsed time since the previous frame.
 func _process(delta):
 	pass
+

scripts/Main Interface.gd

 @onready var second_scores = []
 
 @export var energy_creator_click_value = 1
-@export var l1_generator_initial_cost = 10
+@export var l1_generator_purchase_cost = -10
 @export var l1_generator_click_value = 1
-@export var l1_analyzer_initial_cost = 25
-@export var l1_analyzer_click_cost = -1
+@export var l1_generator_mult = 1.15
+@export var l1_generator_num = 0
+@export var l1_analyzer_purchase_cost = -25
+@export var l1_analyzer_click_cost = -2.5
+@export var l1_analyzer_mult = 1.25
+@export var l1_analyzer_num = 0
 
 signal interface_ready
-signal score_update(value)
+signal score_update(value: float)
 
 # Called when the node enters the scene tree for the first time.
 func _ready():
 	# This is set in inspector options, but just in case.
 	messages.narration.json_content = get_json_file_content(messages.narration.lines_file_path)
 	click_target.buy_l1.visible = false
-	click_target.buy_l1.text = "Add L1 Generator (costs " + str(generators.l1.cost) + ")"
 	print("Emitting interface_ready signal.")
 	interface_ready.emit()
 	
 	pass
 
 func update_score(new_score):
-	messages.score.update(new_score)
+	score_update.emit(new_score)
 	if messages.score.total_score == 1:
-		await get_tree().create_timer(0.5).timeout
-		messages.message.show_message_by_id(2)
-		await get_tree().create_timer(1).timeout
-		messages.message.show_message_by_id(3)
+		pass
 	elif messages.score.total_score == 10:
-		await get_tree().create_timer(0.5).timeout
-		messages.message.show_message_by_id(4)
-		await get_tree().create_timer(1).timeout
-		messages.message.show_message_by_id(5)
-		await get_tree().create_timer(1).timeout
-		messages.message.show_message_by_id(6)
-		await get_tree().create_timer(1).timeout
-		messages.message.show_message_by_id(7)
-		await get_tree().create_timer(1).timeout
-		messages.message.show_message_by_id(8)
-		await get_tree().create_timer(1).timeout
-		click_target.buy_l1.visible = true
-		messages.message.show_message_by_id(9)
-
-
-func _on_add_item_target_pressed():
-	if messages.score.current_score < autoclicker_cost:
 		pass
-	else:
-		generators.l1.click_value += 1
-		if not generators.l1.l1_auto_display.visible:
-			generators.l1.l1_auto_text.text = generators.l1.text1 + str(generators.l1.click_value) + "x" + generators.l1.text2
-			generators.l1.l1_auto_display.show()
-			generators.l1.start_clicking()
-			messages.message.show_message_by_id(10)
-		
-		messages.score.update(0 - autoclicker_cost)
-		autoclicker_cost = (autoclicker_cost * 1 + (generators.l1.click_value)) * 1.5
-		click_target.buy_l1.text = "Buy Autoclicker (costs " + str(autoclicker_cost) + ")"
-
-func _on_sps_timer_timeout():
-	if len(messages.score.prev_second_scores) >= 5:
-		messages.score.prev_second_scores.pop_at(0)
-	messages.score.prev_second_scores.append(messages.score.current_second_score)
-	messages.score.current_second_score = 0
-	var avg_score: float = messages.score.prev_second_scores.reduce(func(acc, c): return acc + c, 0)
-	current_per_second_score = avg_score / len(messages.score.prev_second_scores)
-	messages.sps.text = str(current_per_second_score) + " per second"
-	messages.sps_timer.start()
-
-func get_text_file_content(file_path):
-	var file = FileAccess.open(file_path, FileAccess.READ)
-	var content = file.get_as_text()
-	return content
-
-func get_json_file_content(file_path):
-	var file = FileAccess.open(file_path, FileAccess.READ)
-	var content = file.get_as_text()
-	var json_content = JSON.parse_string(content)
-	return json_content
 
 func _on_message_timer_timeout():
 	pass # Replace with function body.
 func _on_narration_end_introduction():
 	click_target.energy_creator.visible = true
 
-
 func _on_energy_creator_pressed():
 	messages.sps.visible = true
 	update_score(energy_creator_click_value)
 
-
 func _on_buy_l_1_generator_pressed():
-	update_score(l1_generator_initial_cost)
+	update_score(l1_generator_purchase_cost)
+	l1_generator_purchase_cost *= l1_generator_mult
 	
+func _on_buy_l_1_analyzer_pressed():
+	update_score(l1_analyzer_purchase_cost)
+	l1_analyzer_purchase_cost *= l1_analyzer_mult
 
+# UTILITY FUNCTIONS
+func get_text_file_content(file_path):
+	var file = FileAccess.open(file_path, FileAccess.READ)
+	var content = file.get_as_text()
+	return content
 
-func _on_buy_l_1_analyzer_pressed():
-	update_score(l1_analyzer_initial_cost)
+func get_json_file_content(file_path):
+	var file = FileAccess.open(file_path, FileAccess.READ)
+	var content = file.get_as_text()
+	var json_content = JSON.parse_string(content)
+	return json_content

scripts/Messages/narration.gd

 func _on_interface_ready():
 	print("Narration received interface_ready signal.")
 	var main_sequence_messages = json_content["main_sequence_messages"]
+	
 	print("Got JSON content keys " + ", ".join(main_sequence_messages.keys()))
 	for section in main_sequence_messages.keys():
 		message_lines[section] = []

scripts/Messages/score.gd

 func update_text(score_num):
 	text = "Energy: " + str(current_score)
 
-
 func _on_interface_ready():
 	pass # Replace with function body.
 

scripts/flag_keeper.gd

+extends Node
+
+@onready var main_interface = $"../.."
+@onready var flags: Dictionary
+
+# Called when the node enters the scene tree for the first time.
+func _ready():
+	flags = {
+		"total_score": {
+			"next": 0,
+			"list": [1,10,],
+		},
+		"current_score": {
+			"next": 0,
+			"list": [],
+		},
+		"narration_milestones": {
+			"next": 0,
+			"list": [],
+		}
+	}
+
+
+# Called every frame. 'delta' is the elapsed time since the previous frame.
+func _process(delta):
+	pass

text/message_lines.json

 {
-	"main_sequence_messages": {
-		"introduction": [
-			{
-				"id": 0,
-				"text": "Welcome to SPARK, the Species Preservation and Reconstruction Kit.",
-			},
-			{
-				"id": 1,
-				"text": "I'll add a button below this text. Please click it once."
-			}
-			], 
-			"get_to_10": [
-			{
-				"id": 0,
-				"text": "Well done! You'll notice that your energy total has gone up."
-			},
-			{
-				"id": 1,
-				"text": "Go ahead and click a few more times. Your target energy is 10."
-			}
-			],
-			"explain_mechanism": [
-			{
-				"id": 0,
-				"text": "Good work. The SPARK click mechanism works a little like an old engine."
-			},
-			{
-				"id": 1,
-				"text": "You have to crank it a few times to get it started."
-			},
-			{
-				"id": 2,
-				"text": "Each click provides a little bit of the energy that SPARK needs to operate."
-			},
-			{
-				"id": 3,
-				"text": "But now that we've got some energy in the bank, we can start the engines up, so to speak."
-			},
-			{
-				"id": 4,
-				"text": "With the energy your clicks have yielded, you can start up an automated generator."
-			},
-			{
-				"id": 5,
-				"text": "I've added a button where you can do just that."
-			}
-			],
-			"bought_generator": [
-			{	"id": 0,
-				"text": "The generator will yield the equivalent of one click per second."
-			},
-			{
-				"id": 1,
-				"text": "You can use your energy to activate additional generators. Their total output is shown above."
-			}
-			],
-			"afford_analyzer": [
-			{
-				"id": 0,
-				"text": "Once you have enough energy stored, you can turn on an analyzer."
-			},
-			{
-				"id": 1,
-				"text": "Analyzers use energy to scan DNA fragments and work out how they fit together."
-			},
-			{
-				"id": 3,
-				"text": "And before you ask, we know all of these fragments are less than a myriad old."
-			},
-			{
-				"id": 4,
-				"text": "They've decayed a bit, but they're still readable."
-			}
+	"main_sequence_messages": [
+		[
+			"Welcome to SPARK, the Species Preservation and Reconstruction Kit.",
+			"I'll add a button below this text. Please click it once."
+		], 
+		[
+			"Well done! You'll notice that your energy total has gone up.",
+			"Go ahead and click a few more times. Your target energy is 10."
+		],
+		[
+			"Good work. The SPARK click mechanism works a little like an old engine.",
+			"You have to crank it a few times to get it started.",
+			"Each click provides a little bit of the energy that SPARK needs to operate.",
+			"But now that we've got some energy in the bank, we can start the engines up, so to speak.",
+			"With the energy your clicks have yielded, you can start up an automated generator.",
+			"I've added a button where you can do just that."
+		],
+		[
+			"The generator will yield the equivalent of one click per second.",
+			"You can use your energy to activate additional generators. Their total output is shown above."
+		],
+		[
+			"Once you have enough energy stored, you can turn on an analyzer.",
+			"Analyzers use energy to scan DNA fragments and work out how they fit together.",
+			"And before you ask, we know all of these fragments are less than a myriad old.",
+			"They've decayed a bit, but they're still readable."
 		]
-	}
+	]
 }