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The first stop for your last mission is the Presidential Metro. You can access it by going to the entrance in the D.C. Ruins. Go over to the marked spot by the East Capitol Building. Go into the utility route and go down a new ladder into the Presidential Metro. If you go to the White House Crater, then you missed the entrance.
The Presidential Metro itself is pretty straightforward. You just keep walking down the tracks. There are some turrets and sentry bots that you have to watch out for during your trip. You should be good at killing them by now. Just charge forward and target their arms in VATS. If you manage to cripple them, then you basically get 5 free seconds to finish them off without taking any damage. Clear a path through the defenders. Your goal is to follow the line until you get into the next office with M.A.R.Go.T. If you don't have much skill in Speech or Science, then you might want to look on the train cars for the Senate ID. You'll find the ID next to a skeleton on a train car right after you cross over from the first corridor to the next. That lets you skip the test. It shouldn't be a problem for any moderately skilled character though. Just save and try again if you fail.
Once you pass the test, M.A.R.Go.T. asks for your help in securing the Presidential Metro. Apparently a whole bunch of ghouls are there. Arm yourself and prepare for one heck of a fight. If you are doing this at a high level, then be ready for a tough fight if you plan to help M.A.R.Go.T. The sentry bots just can't handle the feral ghoul reavers that show up on high levels. You can barely handle them, thanks to the tight space. The only real hope is that they will pointlessly attack the turrets and expose themselves to a lot of attacks.
You don't have to clear the Metro. If you want, then you can just put on the ghoul mask and go forward to the end of the tracks. There will be one sentry bot by a fuse box and the train car. You can just kill him to get the fuses. It's a simple repair task to pop the main fuse in and start the car. If you kill the ghouls, then M.A.R.Go.T will thank you and the sentry bot will take care of the repair for you.
Get into the train car and start your journey. You'll end up at Adams Air Force Base.
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It's time to quickly get your new toy before the Enclave figure out that you're here. Kill the few soldiers and start walking toward the marker. Go around the back of the nearby control building and look for the large box. Pick up the Tesla Cannon and the ammo here. Grab the orders to learn about Tristan's plan and trigger the Brotherhood of Steel assault on Adams Air Force Base. You are taking the brunt of the punishment though.
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Reaching the Air Traffic Control Tower
Your ultimate goal is to get to the Mobile Base Crawler. It's a long battle and you'll be up against a ton of Enclave soldiers and several clusters of turrets. To be honest, the battle is basically open to your decisions. It's a big open field and you have a lot of options. You can sneak around to ambush soldiers. You can hack terminals and make the turrets shoot at the Enclave too. Your new Tesla Cannon is naturally a gift from the heavens. You'll be able to blow up Vertibirds in one hit and kill a number of Enclave Soldiers in one or two hits. There are some artillery positions early on that you can use, but Ii personally think it's better to just play around with the Tesla Cannon for now.
Your mission at the moment is to just reach the large air traffic control tower so that you can get the entrance ramp for the Mobile Base Crawler to lower. The path is fairly easy to see. Just go down the path between the buildings. Kill each patrol of Enclave. There are roughly 3 or 4 in each group. You should be good at killing Enclave at this point. Go through the deathclaw cages. That's roughly the halfway point. You can unlock the cages if you want, but you usually end up fighting the deathclaw at the end of the fight, so it's of questionable worth.
The last bit just requires a bit of skill and luck to take out the few bunker positions. It's then just a matter of getting into the tower. Go up the stairs and enter the marked door. Kill the sentry bots inside and go up the staircase. Leave to go into the main tower which overlooks the airfield. Access the terminal to lower the ramp. Then get out of the tower. Some vertibirds are coming and they will use their missiles and bombs to try and take you out while you're in the tower.
Go out and rush across the field to the Mobile Crawler. I shouldn't have to explain the rest of this. Keep shooting and do what you can to take out the Enclave still guarding the field and the Crawler. Rush up the ramp and get into the Crawler.
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Mobile Base Crawler - Evening the Odds
Alright. You're actually pretty close to done. Some quick lessons though.
The blue fields are stasis fields. You have three options to get through. If you have 80 Science then you can completely disable them. If you have 50 in Explosives you can use a timed charge. You can also just smash the console, but the resulting explosion always hurts you. Blowing it up also only weakens the field. It will burn you as you cross it.
The left goes to a bunker/armory for the elite Enclave that are apparently waiting for you to show up. Don't go that way just yet. Going to the left triggers an alarm which causes the barracks to empty and makes you fight 6 Enclave in close quarters. Go to the right and talk to Stiggs. Be nice and he'll explain the entire layout to you and tip you off about the mainframe that's just above you. That's your goal for evening the odds right now.
Go up the stairs to the right and get to the second level. Follow the optional marker and start navigating the platforms. You should be able to find and kill any one of the Enclave officers here. Grab the keycard off of them to gain access to the mainframe. Kill any soldiers in here and hack the terminal. If you have 75 Science then you can also hack the robotics terminal to shut down all the turrets and robots. That makes everything much easier. Here's the best part though. If you have the Robotics Expert perk, then you can actually reverse the IFF codes on the robots and turrets. All of them are now your allies. If you do this, then you will be able to just sit back and let your new robot army kill half of them. Go ahead and unlock all the doors and the armory. That's your next stop.
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Mobile Base Crawler - Finishing Up
Time to wrap things up. Go to the armory first. You probably want the equipment. Go across the level to the left side and go back down the steps. You won't have to deal with anyone besides the Enclave now that the robots are on your side or shut down. Just go along and kill the Sigma Squad soldiers here. Should be about 6 or so. The real prize is down in the armory. Go inside and search it for just about every weapon in the game. Stock up on ammo and look for the ammo boxes on the middle of the table. There should be a good number of power cells for the alien blaster. There is also another alien blaster in here too, but one of the Sigma soldiers usually grabs it, so search the bodies.
After that, you're pretty much done. Grab what you want and go back up. I suggest you just avoid the deathclaw pins. They don't help much and it isn't really worth it. Then just keep going up and out onto the platform. There's another big battle up here. Take out the vertibirds as they land to even the odds up a bit. Then just use the cover of the platforms to pick off the Enclave. Keep moving up and enter the Satellite Control Tower.
It's one more fight before the end. Start pushing up the stairs. There are another 6 or 8 Enclave in here, but they shouldn't be a threat anymore. Your real goal is to get to the top and reach the terminal here. This is the end. Before you commit to anything, you need to be sure that you got what loot you wanted from the Crawler and the Armory. They are sealed off after this mission. When you are sure that you're done, access the terminal and get ready to make your choice.
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Who Dares Wins - Wrapup and Aftermath
Choose Adams Air Force Base
A standard end to the mission really. You will get 1000 points of good karma, so expect a possible reversal for evil characters. Go out and get picked up by an awakened Lyons and her rescue squad. She'll take you to a nearby viewing platform and you get to watch a really cool explosion. Get back inside after its done to go back to the Citadel and receive their thanks and a mission complete.
Paladin Tristan also has a new mission. You can effectively receive a bounty for killing Super Mutants, but you're probably past any real need for caps by now though.
This one is obviously bad. You get 1000 points of bad karma. Sarah Lyons will fly you back to the Citadel and just assume that there is a problem with their radio when they don't respond. You will arrive to a destroyed Citadel and a bunch of angry survivors. Lyons figures it out pretty quick and attacks you. Kill her and the group of survivors left behind. You can go inside and search the hidden Brotherhood of Steel armory locked inside the ruins of the Pentagon. The door is near the old target range. Go in and look for the safe in the wall. You can get a unique magnum called Callahgan's Magnum and a good bit of alien power cells.
The Brotherhood doesn't take this well though. Any Brotherhood of Steel soldiers in the Wasteland will shoot you on sight.
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This concludes the main quest in Broken Steel. Most of the side quests are shut off if you blow up the Citadel, so I hope that you took that into consideration.
For now, you can just go about your business in the Wasteland. There's a bounty for Super Mutants and you now have a giant cannon to play around with. Have fun and wait around for more DLC.