Let's break this Marvel awesomeness down:
Phase 2 will "end" with Ultron and the world reeling. Through various sources, there is a major rift between the Avengers, leading to the creation of a new team under Captain America at the end: Banner loses control and can't be trusted; Thor distrusts Stark and returns to Asgard; Captain America has a falling out with Iron Man over pre-emptive policing (much like The Winter Soldier); etc. This paves the way for Phase 3.
Ant Man is starting to look like an extended Marvel one shot, as there was no announcement of a sequel (even though it's STILL filming, and GotG didn't even get a sequel until it was done being edited…so, grain of salt). The way Feige announced the movies yesterday, it appears that Ant-Man closes out Phase 2. Maybe a callback to the original creation of Ultron that Stark "revives?"
Anyway, on to Phase 3:
Captain America 3: Civil War – Cap is searching for The Winter Soldier, and Iron Man finds out he was responsible for Howard and his mother's death (as revealed by Zola in The Winter Soldier). Cap and Iron Man have words, while a minor character (Hawkeye, maybe Falcon) gets into it with Crossbones, which causes civilian deaths. This leads Stark to back the government's Registration Act, which calls for all "heroes" to be registered and policed. Who is watching the watchmen? Cap finds Bucky, brings him back to normalcy, and together with Falcon and Black Panther's outside input, convince Stark that he was wrong. Meanwhile, Crossbones gets a drop on Cap and the movie ends with him potentially assassinated.
Dr. Strange – This introduces mysticism to the Marvel Universe. Treat this like Guardians of the Galaxy, and only have passive references to the greater post-Avenger world, with direct references to Ultron. It is revealed that Dr. Strange's powers are derived from the Soul Gem, but he does not know it.
Guardians of the Galaxy 2: If the rumors are true, then Hulk might get launched into space at the end of Ultron by someone (Stark? Ultron? Banner? Who knows…). This movie introduces the idea of the Nova Corps rebuilding and answering the question of Star Lord's origins. Drax and Gamora are still after Thanos. Thanos is involved, attempting to retrieve the Power Orb from Quill (He doesn't know the Nova Corps has it…yet). At the end, Quill's dad is revealed, Thanos gets it from the Nova Corps, and during a end-credits scene the Guardians find Banner in a cell in a fighting ring, and agree to bring him back to Earth.
Thor 3: Ragnarok – Thor returns to Asgard, and realizes Loki has been impersonating Odin for some time. While Thor attempts to reveal Loki's betrayal and restore order to the Throne, Ragnarok arrives. Thor, Loki, and the recently saved Odin must fight together to preserve Asgard. However, although it is the first time Ragnarok is avoided in Asgard's history, Thor and Loki "die" leaving Odin reeling, looking for a new heir. Thanos gains possession of the Infinity Gauntlet and the Tesseract (which was in the Vault). Bonus Post credit scene: BETA RAY BILL
Black Panther – Following the events of Ultron and Civil War, T'Chaka decides to end the isolationism of Wakanda and introduces it to the World. Black Panther must deal with newly focused outside influences to preserve the great nation, at his own personal expense. Cameos of Black Widow and Hawkeye helping Black Panther (who does not accept it, initially) are a plus. Maybe the Time Gem is introduced in an end credits scene, which explains the Wakanda Panther God as being a being with access to the Time Gem, and all that it entails.
Avengers 3: Infinity War Part 1 – Thanos has the Gauntlet and Tesseract, but no other stones. He obtains the Aether from the Collector, comes to Earth, and obtains the Staff from Stark (who gets it following Ultron and gives it to the USA), Time Gem (from Wakanda), and Soul Gem (from Strange) completing the trifecta. The Avengers come together, and are absolutely decimated by Thanos. Thanos erects his new palace and throne on Earth. End Credits: Guardians arrive in Earth orbit and realize Thanos beat them; Carol Danvers is injured in the fight, and gets her DNA mixed with a Kree.
Captain Marvel – Following the fight, Carol Danvers travels off world to learn of her powers, and becomes Captain Marvel. Instead of being the successor of Mar-Vell, she finds Mar-Vell who teaches her how to use her powers. End Credit Scene: She returns to Earth and finds the Guardians in a hidden orbit behind the moon, and they decide to work together.
Inhumans – Terrigen Mist is introduced, and many people start to express their abilities. Lockjaw leads a local fight against another faction of Inhumans who want to work with Thanos, and many Inhumans are introduced to the audience. It is confirmed that Skye is an Inhuman, and her father was part of the faction that wants to help Thanos. Thanos knew of the Inhumans all along due to his Deviant heritage. Lockjaw and company prevail, and prepare to confront Thanos.
Avengers 3: Infinity War Part 2 – Thor returns to Earth, as he was not "killed" but banished from Asgard. The original Avengers team up together and bring their friends (Falcon, War Machine, Black Widow, Hawkeye, Pepper Potts (fired up) etc.) and join with the New Avengers (Ant-Man, Dr. Strange, Black Panther; The Secret Avengers (Agents of SHIELD, Defenders); The Guardians of the Galaxy; and Captain Marvel, for an end all war with Thanos. The Gauntlet is corrupted by someone (Captain? Captain Marvel? Quill?) and Drax gets to Thanos for a final throw down. Drax gets his revenge but is presumed dead. Thor, Stark, and Captain America die. Thanos is defeated (but not killed) and disappears. The New Avengers vow to rebuild and protect not only Earth, but the Galaxy as well.
So far, to me, this is what it looks like is going to happen through Phase 3.
