You could present the game in a more reactive fashion.
If the players do not appear to be making any kind of indications of the sort of actions that they would like to take then you could simply present low-importance information back to them and again prompt them for action.
For instance: The players would like a means of entering a city and have their reasons not to do so in conventional ways (through the front gate - through the guards).
You could start be describing the city as being... "...on a slope, with most battlements appearing to be well-maintained, the grey slate mostly devoid of growths and only the faint shadows of the sun high in the sky betraying the existence of minor weather erosion. The breeze blows warmly across the landscape and activity at the gate seems calm."
In the lack of an indication of action you could prompt the group with the soft suggestion - "Would you like to explore further?"
(Side Note - if the response is something as low-brow as "we wait a little to see what happens" then an appropriate response could be "You wait a few minutes and watch as a small flock of pigeons rise and fall in the distance over the rafters... Nothing of further note catches your attention. What would you like to do now?" This presents the low-importance information mentioned earlier - unless there is good reason to add information (a time-line like an approaching storm or a nearby threat))
If yes then "OK. Tell me who in the group is going to be exploring and in what manner. Are you looking for anything?"
And in response to the lackluster "Looking for a way in" - "OK - You need to tell me specifically what kind of way in you are looking for and how you are going to do it"
This will engage the players and certain avenues may present options to you. Perhaps scouting the walls in a careless or unstealthy manner might result in a challenge from atop one of the watch towers. Or perhaps they will happen upon a small group of shady characters with which interaction might occur.
You may also be presented with options that you had not considered.
A search of the walls for a means to scale it might reveal a particular location between battlements where external plumbing has been affixed externally to the wall, leading downwards and terminating a short way above a lonely sewage wagon. This would present the possibility of an easier climb DC should they choose this way to enter - although there is no guarantee that it will not be detected or that it will be safe. The small stream inlet further north around the city (assuming that the character searches further) might prove a better bet - especially if you can swim.
Although the players needn't be told that unless they test the waters first - that is part of the fun of being a GM - you don't need to worry about common sense on behalf of the players - you can provide warnings of difficulties if you wish.
In this way you are presenting the kinds of choices that the players elicit from you. If they don't appear remotely interested in going through the gate then there is no need to present the hint (if specifically searched for) that the guard might accept a payoff - or that disguises might work due to the apparent lazy disposition of the guards in general.
Of course you will occasionally want to prod the group if they end up in a situation with no clear way forward. If boredom is setting in and the group is stuck looking for posters of jobs at the guard house then perhaps their attention might be drawn to a short old man who watches them intently from outside the door. That may play out in various ways - whether to present a task or to present a new foe or to direct the players to a location that they would be more likely to find work.
Alternatively it is possible to draw upon the characters' background history - a little clue that occasionally pops up here and there. Whether it materializes as expected is not important - it helps to provide direction and direction is a precursor to momentum.
Presenting secondary events
When you spend time designing secondary plots for the party to stumble upon it is understandable that you would 'wish' for the party to stumble upon them even if they might not otherwise do so.
While you could certainly place all these encounters (conveniently) in the path of your players, there are several factors to consider:
- Conservation of effort and resources - Is it of particular importance for the players to encounter this sub-plot at this juncture of the adventure? You could perhaps look at different ways to capitalize upon the players missing this plot-line and any reasonable clues (such as the occasional unexplained whiff of rotten meat - or a suspiciously intact section of skeleton laying near a dump site in the sun (perhaps waiting for the dark to saunter its way toward an evil source)) that you might have placed in their path.
Would it be economical for this basement-dwelling dabbler necromancer to 'move' to a run-down shack in an unnaturally silent part of the forest (think 'Evil Dead')? Or perhaps a next town if the concept would work better in an urban environment.
One last possibility is introducing the possibility of consequences for events that are not encountered and tackled. Perhaps failing to notice the dabbler necromancer would result in an increased incidence of undead attacks in the surrounding country-side as his poorly contained energies seep away and awaken a worse evil than he or she could ever have imagined. This could also apply to the potion shop ruckus - a few ill-mixed ingested potions could release a crazily mutated humanoid upon a rampage.
Suspiciously peaceful aftermath - If your players encounter nothing but resistance from varying seemingly unrelated forces before completing the main event, and emerge to sunshine and rainbows within a suddenly peaceful city then one or two players might begin to suspect that one or more secondary plots were contrived - placed before them - possibly denting the suspension of belief that goes with good role playing games (its not so likely if they actively pursued reasonably challenging and scarce clues). Even if you don't happen to have any good secondary plots left for this city you could always fall back on the consequences of the breakdown of the structure of order in part or all of the city (The guards are distracted. Looters ahoy!).
Player conditioning towards proactive approach - If the players do not express any desire to explore the rest of the city then they do not have to. Once again you can recycle materials for other locations in terms of shop descriptions and the like (just be sure to keep track of what NPCs and places you put in which locations - jot notes on the fly). Furthermore you could occasionally tease the players by having a couple of travelling NPC casually comment between themselves that "The 20% sale was a novel idea", or that the "Artifact auction was popular" or that "Villagers have started disappearing in the night", etc.
Eventually the players may get the idea that it is worthwhile to get a small idea of a city as you never know what you might find.
Hint - If you are not into detailing maps then you could do worse than to set all the locations (or clusters of locations) on a probability chart. If they roll successfully for a particular location then you could describe that section in shallow detail similarly to when you described the city at first sight - let them explore and direct the flow. Rerolls can attempt to avoid areas already explored - alternatively a good streetwise test (even characters can get lost in some places that are big enough).
Conservation of energy as a GM
While some of these thoughts may hopefully prove useful to yourself in conducting your games, remember that they are a set of suggestions that need not be implemented in full. You will find it desirable to determine how deeply you wish to describe your world and an excess amount of it may be pleasing but it may also entail a greater degree of creative involvement on your part. This is why I mentioned certain time-saving elements like use of pre-determined probability charts - these are tools intended to take a little of the burden off your mind - but should not serve as an obstacle to your doing what you wish to do (you can fudge a roll or allow direct movement if it takes your fancy) - after all, the tools serve you, not vice-versa.
You're in quite a difficult situation. Your players don't have information, don't have many leads, have one dead party member, and have been launched into confusion.
Slow down the overarching plot of your game - grind it to a halt for now, if you need to. Your players (and their characters) both are not ready for it and do not have the information they need to process it. The way this game is being played, you have significant control over the plot and pacing of the game. Slow, possibly to a halt, the destruction of the universe and the whole ancient magicks and dragons shindig. Your players know it's an imminent threat, but lack the skills or knowledge they need to confront it in any way - they need time to learn and grow.
In a lot of ways, this can serve simply to set the scene for whatever else is going on, and contextualize the additional information the players gain from other goals and quests. Let it do so - your players will learn about the overall problem, and potentially be able to connect the dots where others have not. At a later time, once the players have better information, they'll be able to handle the overarching plot. Until then...
Give your players information. Consistently, the examples you've communicated have had a common problem: the players achieve what they in the scene want, but don't get any information about what they want in the broader scope. There are two effects from this: first, the players will grow frustrated; second: the players will quickly run out of leads. The leads they get need to go somewhere.
Maybe occasionally you can throw in some lead that just doesn't work, but the majority of them should provide some sense of success. The players learn something, or gain something. They don't have to completely understand it, but something needs to happen. Otherwise, all the plot hooks will drop. For instance, while interrogating the cultists, some design element of this scene needs to provide the characters with more information about who and what they want to be pursuing.
Always ask yourself, "Would the players really enjoy this right now?" - and give a more detailed answer than just yes or no. For instance, concerning the meteor falling, ask yourself, "Would the players enjoy the meteor falling right now?" The answer to this question is, as you've retrospectively identified, something along the lines of "No, because the players do not have the information or skill they need to handle the situation."
You've got a good scene - meteor falls, chaos ensues - but the players aren't prepared to handle it in a way that makes the game fun for them. If the game were run again, this scene should be saved for a time when the players can deal with it in a meaningful way. By answering the "is it fun?" question, you've learned two areas which must be fulfilled before you can safely play out this scene: the players need to be more powerful, and the players need more information. Once the players have achieved this, then you can go and run this scene.
Obviously, this scene has already been run, and I'm only using it as an example. Short of rolling the game back to before this scene (which may be a completely reasonable course of action, depending), this is part of the game world right now, and is just something the players are going to have to deal with.
This is the core of my advice. But how does it apply to your campaign?
Here's what I'd strongly advise: set aside things the players can't handle for now. They can evolve in the background, but as a general rule, they shouldn't affect the players until they're ready to be drawn into those plot threads.
Come up with some scenes that your players would all want to play, and would all be able to handle, and draw the characters into them. Your players will decide what they want to do next, and it's probably going to be to explore deeper. Through these scenes, you can feed them pieces of information, ideas, thoughts, and leads, which will draw them both a) into more power through the experience system, and b) into greater understanding of the forces at work in your game.
The word that comes to my mind is 'ALLIES'.
The ally is an NPC that wants (or needs) the group. They can help in three ways
A) Offer themselves to the group as a wandering helper. A person who wants to travel to the city you are going to will welcome the extra security.
B) Offer them equipment to help the part. It could be a character's parent (mum!) passing on a family heirloom magic sword, etc.
C) Offer them help with contacts throughout the realm. If an old wizard has asked the party to gather ingredients from another town, then there is no reason that the wizard doesn't have friends in the other town. Someone roughs you up when you go to pick up the the ingredients, and suddenly the local wizard guild comes to the rescue.
My rule of thumb for lightening a session up is to have the NPC do two things: be funny with an outgoing personality that makes them very likeable, and allow them to crack a joke at the best (or worst!) of times.
The other thing this NPC needs to do is to somehow show a display of power; if your brother joins the group and he is a peace loving monk then have him beat up the local bully, afterwards he turns to you and says 'they did teach us to fight as well as flower arrange you know ... '