I agree that it'll open with a "prelude" mission with Cap, Widow and Rumlow against Batroc and his Brigade (incl. Machete) on a Roxxon Oil tanker. Dunno if that will play into the larger plot or just be one of those 007 style intro pieces, but we'll see. If it ties in, then I'd guess Batroc is HYDRA as well.
We then go through a lot of "downtime," action-wise, as Cap meets Pierce and the lovely Sharon Carter (who isn't identified by her real name initially), befriends Sam Wilson, gets pretty friendly with Natasha, and buddies up with Brock Rumlow. There's a lot of "fish out of water" adjustment comedy/drama going on in this section with Steve as the "soldier out of time." Also, political tensions are building within SHIELD, as former friends Fury and Pierce begin to clash on policy and strategy issues. Steve begins to feel misgivings and mistrust towards SHIELD, and senses that all is not right in the hallowed halls of the Triskelion.
Out of nowhere, a super-powered assassin rises with a team of mercenaries and carries out a major hit against Nick Fury, in a spectacular running gun battle through the streets of DC, and very nearly succeeds in his assignment. Fury is hospitalized, and Hill takes over at SHIELD. The assassin(s) isn't through with Nick Fury yet, and comes after him again in the hospital to try to finish the job. Cap and Black Widow are able to stop him, but Fury and Steve agree that it's best for Fury to lay low and pretend to have died in, I dunno, an explosion or something at the hospital. Yeah, it's TDK all over again, but what are ya gonna do.
So Cap and Widow put on their detective caps and recruit Sam Wilson to their Bloodhound Gang. They try to track down this mystery assassin, learn more about this Winter Soldier, dig deeper and find out that HYDRA has quietly re-emerged in the modern world and has infiltrated the highest levels of SHIELD, government, and world power. As they pry farther, they find secrets that date back all the way to WWII, with some very familiar names and faces from Steve's past popping up in unusual places. HYDRA has basically continued unchecked from the days of Red Skull, with the traditions carried on by men like Arnim Zola and Baron Von Strucker.
Having gotten too close to the truth, Cap, Widow and Falcon become the hunted themselves. Even former friends and associates, like Brock Rumlow, are trying to kill him. The ever-widening conspiracy envelops the heroes at every turn, culminating in a final climactic battle which will pit Steve against his closest friend from the past. Once he "turns" Bucky back and deprograms the brainwashing, together they're able to unmask Alexander Pierce as the brains behind the HYDRA conspiracy. (I have no idea who Pierce will really be; I just know there's plenty of viable options there, and he most definitely will be a recognizable comic-book archvillain from Cap's mythology.)
But unmasking isn't the same as defeating the enemy. I don't think there's a happy ending here. In keeping with the 70s political thriller vibe the Russos have said they're aiming for, I suspect it ends on a down note, with the villains still in charge. I suspect that HYDRA will "out" themselves at the movie's end, and we'll essentially see HYDRA holding the world hostage. The movie ends with Cap realizing that the only way to win is with the Avengers as their own unit; and so he rallies the Avengers one more time, even enlisting the aid of some emerging superheroes, and prepares for war against his oldest enemies, and against the deadliest weapon in their arsenal....
....a robot called ULTRON.