My players are in a predicament and I don't know how to run it mechanically next session...

Last session one of my players, through lots of legitimate work and effort, obtained a captain's position in the military and is now in charge 5 soldiers and has to keep them moving from point A to point B along with an legion of soldiers. The entire legion, about 750-1000 soldiers, is moving through a forest and has to rest during the night. They are scattered and travelling in groups of 5-10, not expecting a fight. During the night the entire forest of soldiers were attacked my flameskulls, about 100 of them. Next sessions my players need to traverse the battlefield and escape the forest.

The thing is, I had no clue about my players were working to gain a rank with the military and travel with them, so i was not expecting this predicament. I had to have the flameskulls attack, it is crucial to the story, but now I don't know how to run their escape mechanically. I can't just have them fight through 100 flameskulls, I couldn't even do another 10, it would take far too long and wear on and on. I need to keep the campaign moving, so my goal is to have them out of the forest within the next 2 sessions, unless they all die. There are 6 of them, all level 4, with 5 npc soldiers. 2 soldiers and 3 players are currently down, so that is where we will pick up next session.

There are reasons why the army is travelling in this manner, because I know a lot of people might make note of that.

Any advice would be welcome, thanks so much!

It honestly shouldn't really be a problem. 100 flameskulls broken up among that many solders is surprisingly few. Each group would only have to deal with 1-2 flameskulls. If they somehow can't deal with that, you don't need to have them fight any. Instead, it could be more like a chase encounter, ducking by flameskulls and dodging spells.

Hmm, I do like the idea of them running through the woods, dodging fire rays left and right, jumping over wounded soldiers and such. Any thoughts on setting that up on my end?

If you want a narrative encounter make the skulls hidden above in the trees and keep the party moving being pursued by the skulls with flame attacks. (these attacks don't have to hit the players, but have them come very close to hitting, exploding trees or causing the brush to catch fire, definitely kill off some NPCs to enforce the urgency of the pursuit)  The players never see the attacks unless they make a very high perception check, but stress that movement is the key to not being overrun. Make it a skill check encounter and let the players decide which skills they want to use and how to use them. Let them think outside the box if they can come up with an off the wall way to use a skill to cover their tracks let them. Three successes before three failures for 1 day of travel from three different PC's, the same PC can't do all three checks, each failure increases the DC by 2 or more(up to you), start at 10 DC (or 12 if you want more of a challenge for the players or depending on the crazy way they are using their skill).  (Only allow the help action for characters proficient in the same skill they are trying to use, if you want). Three failures result in a con saving throw to avoid a point of exhaustion (based on the DC they accumulated) and maybe some damage taken by each member of the party, Or it forces a fight with a small number of flameskulls( or owlbears, bears, wolf pack, there are other dangers in the forest I imagine) just enough to drain some resources, the creatures attack for 3 rounds then retreat.

This will last about one session, if you keep the players harried and running for 2-3 sessions this will really break their morale and make the whole encounter not fun.  No one wants to spend 2 weeks (if you meet once a week) running away from fights being chased, they will get fed up and turn to fight, damn the consequences if it lasts that long.

So:

• Skill challenge, Three successes before three failures per day of travel.  Failures result in increased DC for remaining checks.
• Allow creative uses for skills, not just survival and stealth.  (Deception to throw their voice in a different area,  Animal handling to create wild animal distractions, so on let their imaginations flow).
• Three Failures result in a con saving throw to avoid exhaustion or forces fight with creatures that withdrawals after a set amount of rounds.
• Three successes allow them an opportunity for a short rest or come across some other feature that helps them, DM's fiat.
• Don't extend for more than 1 session, this can have serious negative consequences for the party, no players like to run away much less for multiple sessions, they will rebel.

I agree it would be best ran as an escape rather than a fight. Main difficulty would be convincing the players to flee rather than stand their ground. Maybe as they are invested in the ranks within the military have them be ordered to by a dieing superior rank. Or have the superior rank planning to hold the flamskulls back so that they can get out and report back to HQ.

Could tie together different stealth task and the odd fight with 1 or 2 that block the way, maybe give opportunities from them to set of some distractions etc. 

A hundred flame skulls should be killed by 700 soldiers.  CR 4 creature, besides the 6 spells they get an attack whose range is 30 ft, so they will be up close and personal with archers.  10 archers each attacking, yeah, those skulls are going down.  But they won't stay down.

They should be told by their superior that they can hold the flameskulls, but they are going to run out of holy water.   Then they will be ordered to go for help an  by god bring back at least 500 Holy Water potions or I will have your freakin balls for BREAKFAST.

I can't tell you how insightful and helpful this has been. I run the session on wednesday, will let you know how it goes.

The use of a slightly narrated skill challenge works well for situations like yours.  Do what Noobiwan suggested and would be hard to go to wrong.  I added a link for a blog that suggested using these in 5e.  It is a chase scene so the idea behind it and yours is pretty similar:

https://dmcapn.wordpress.com/2019/04/25/using-4e-skill-challenges-in-5e/

And I had to add something to the thread so I can get notification on how it went!

I second the skill challenge idea.

Okay, I REALLY like the idea of running a skill challenge. Gonna do some prep work and I will definitely check in and let everyone know how it goes. Thanks for all the help!

I have not done a skill challenge myself yet (I have one planned for overland travel soon), but I have watched both Matt Mercer and Matt Colville run them and they looked super fun for both the DM and the players both times.

They are. I like skill challenges, especially for puzzle portions of adventures. Instead of a cross city run they were hunting clues in a library.

My advice would be don't resolve all the combat mechanically. It's too time consuming to handle 20-100 small skirmishes, especially if you actually account for environment, initiative, etc. I think you could do a skill challenge, which would be one thing that I think is usually good for avoiding combat situations, but I don't personally think that fits super well with a combat scenario like this because it is basically a clash between two military forces (at the scales you have in this scenario). I would suggest handling it tactically and tossing the strategics out of the window. Focus on your party and find a way to rally the army together- a skywrite spell from a legionnaire mage, a scouting column riding between pockets, etc. I would focus on forming the army into a spearhead and moving them through the forest or creating an impromptu encampment and settling in for a longer fight. Then, as a DM, calculate the casualties taken from stragglers who can't form up and escape or who were defeated by the flameskulls. An advantage to this is that you can use this to "rescue" your player characters, as they can be at the core of the restructuring, so you don't have to commit to a party wipe if you really want to avoid one and you can even find a way to secure a long rest if you want to dig in and repel the flame skulls (remember that monsters have the fog of war too- if, as a DM, you're playing your monsters as omniscient not only is that unfair to your players, you're also throwing away some of your best options for storytelling and balancing encounters). Flame skulls are kind of nasty, especially for a level 4 party, so I would definitely focus on pacing them out and throwing tons of soldiers at them. Remember that the flame skulls are probably spread out and vulnerable to certain maneuvers as well- they may be slow because there's only a single necromancer giving them orders, or disorganized because they don't have a leadership structure and can't properly engage pockets of resistance in force. Don't make your PCs fight the swarm alone. The army should be engaging throughout the forest and even if the PCS were the first encounter, it should be apparent that there's trouble from smoke and sounds and reinforcements shouldn't be far away.

I also a agree that a narrative skill challenge is ALOT of fun, I try to mix things up in my games and not have constant fighting, but rather sprinkle exotic gameplay here and there. Some puzzles is also usually very fun to play both for the players and you the DM. 

As an alternative, since your setting is currently in a forest, you could have the players come across (or even fall inside) some form of underground structure. Could be an old sunken temple, could be some cavern-style that can lead the players out of the forest to rejoin the rest of the troops. This could give you a world of possibilities on what gameplay you'd like to have your players experience in those tunnels/rooms.

Hitting the players with something unexpected is always welcome and it gives you a chance to switch things around a bit. Maybe you have them solve a puzzle in order to progress down that path and solving that puzzle means they will be safe from their pursuers, so that gives a timer effect to your puzzle sequence. Then, as they are safe, they can either rest a bit to gather their forces and that means they will be ready for more challenges. Roaming monsters could be present (or not), the rest is completely open to you and the players to explore. 

Remember, as the DM, if ever your characters find themselves stuck in a hard situation that only seem to offer one path, you have the power to open a completely unforeseen and unexpected path :)

Simply put, what I do for large battles is have a tiny fraction of the enemies fight the players -- as they are a tiny fraction of their army. Have an appropriate small amount of flameskulls attack the players, and say a sentence or two about the guards desperately trying to avoid being murdered by the rest of the flameskulls. If its too easy, have a flameskull or two fly over fresh from mauling suprised soldiers. If it is too hard, have a scout/guard rush over to aid a commanding officer.

No trouble.

The other thing you can do, if you have Colville's Strongholds and Followers, is make units -- a Soldiers unit and a Flameskull unit. Then let the players control the soldier unit, and you control the flameskulls. On each round of combat, while the players do their actions fighting a handful of the skulls on a battlemap, off stage, the two units are engaged in army combat. The players will decide what their unit does (attack, retreat, etc) and roll for it, and the DM does so for the flameskulls. The units go on the same initiative order as the player-vs-monster combat. If one side outright wins on the battlemap, that side also wins the unit combat and the opposing unit flees (or is destroyed). 

I did this to pretty good effect in the opening scene of my current Roman Empire campaign, and the players enjoyed it. It allowed me to have a wider battle happening, zombies against a Roman century and some temple priests, while the PCs could fight their own battle in the forum against 3 or 4 individual zombies.