I added a simple /sun = storm(false) command, but when I ran this happened:

10:39:34 [SEVERE] java.lang.NullPointerException
10:39:34 [SEVERE] at com.sk89q.bukkit.migration.ConfigurationPermissionsResolver.hasPermission(ConfigurationPermissionsResolver.java:104)
10:39:34 [SEVERE] at com.sk89q.bukkit.migration.ConfigurationPermissionsResolver.hasPermission(ConfigurationPermissionsResolver.java:99)
10:39:34 [SEVERE] at com.sk89q.bukkit.migration.ConfigurationPermissionsResolver.hasPermission(ConfigurationPermissionsResolver.java:99)
10:39:34 [SEVERE] at com.sk89q.bukkit.migration.ConfigurationPermissionsResolver.hasPermission(ConfigurationPermissionsResolver.java:99)
10:39:34 [SEVERE] at com.sk89q.bukkit.migration.PermissionsResolverManager.hasPermission(PermissionsResolverManager.java:102)
10:39:34 [SEVERE] at com.laytonsmith.aliasengine.Script.eval(Script.java:208)
10:39:34 [SEVERE] at com.laytonsmith.aliasengine.Script.run(Script.java:116)
10:39:34 [SEVERE] at com.laytonsmith.aliasengine.AliasCore.alias(AliasCore.java:88)
10:39:34 [SEVERE] at com.sk89q.commandhelper.CommandHelperListener.runAlias(CommandHelperListener.java:88)
10:39:34 [SEVERE] at com.sk89q.commandhelper.CommandHelperListener.onPlayerCommandPreprocess(CommandHelperListener.java:132)
10:39:34 [SEVERE] at org.bukkit.plugin.java.JavaPluginLoader$5.execute(JavaPluginLoader.java:272)
10:39:34 [SEVERE] at org.bukkit.plugin.RegisteredListener.callEvent(RegisteredListener.java:58)
10:39:34 [SEVERE] at org.bukkit.plugin.SimplePluginManager.callEvent(SimplePluginManager.java:338)
10:39:34 [SEVERE] at net.minecraft.server.NetServerHandler.handleCommand(NetServerHandler.java:730)
10:39:34 [SEVERE] at net.minecraft.server.NetServerHandler.chat(NetServerHandler.java:701)
10:39:34 [SEVERE] at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:694)
10:39:34 [SEVERE] at net.minecraft.server.Packet3Chat.a(Packet3Chat.java:33)
10:39:34 [SEVERE] at net.minecraft.server.NetworkManager.b(NetworkManager.java:226)
10:39:34 [SEVERE] at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:89)
10:39:34 [SEVERE] at org.getspout.spout.SpoutNetServerHandler.a(SpoutNetServerHandler.java:436)
10:39:34 [SEVERE] at net.minecraft.server.NetworkListenThread.a(SourceFile:105)
10:39:34 [SEVERE] at net.minecraft.server.MinecraftServer.h(MinecraftServer.java:454)
10:39:34 [SEVERE] at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:363)
10:39:34 [SEVERE] at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)

It appears as though you are not using any Permissions provider, or you are using an odd one. In theory, CommandHelper should work without Permissions installed, but I've found that it doesn't work properly without Permissions installed. Try installing that, and see if that fixes your issue.