Plot encounters are triggered by a certain set of circumstances, and always take precedence over other kinds of random encounters.
Darkspawn Ambush!
Trigger: Player has to become warm with Wynne, make sure she is in your party, and talk to Wynne about abominations. One of the next major random encounters should be this one.
Map: Hillside Path
Description: It starts out as a very typical darkspawn encounter, but it ends with Wynne collapsing and showing something else is wrong.
Actions: Fight and defeat the darkspawn. On the way out of the area (to the north) Wynne will stumble and collapse. She says it's nothing and she'll talk about it later. To follow up with her, talk to her again at the camp, and push the topic.
The Dog
Trigger: If the player is not a Human Noble and saved the Mabari Hound in Ostagar, this occurs as a random ecounter just prior to Lothering.
Map: Plains/Highway Road
Description: If the player has not obtained Dog as a companion from the Human Noble origin and has cured Dog in Ostagar, the party will encounter Dog being chased by darkspawn on the way to Lothering.
Actions: Simply fight the darkspawn and rescue Dog. If you would like to invite Dog to accompany you, you can do so in the conversation with him after the fight. This is the only opportunity to get Dog in your party if you are not a Human Noble.
Harassed from the Past
Trigger: This is part of Leliana's personal quest. After she talks about Marjolaine, the next major random encounter should be this one as long as Leliana is in the party.
Map: Forest Stream
Description: After discussing Marjolaine, the player is ambushed by assassins.
Actions: Defeat the assassins. The leader will surrender and give you the next lead to search for Marjolaine in Denerim. You have the option to kill him. Aside from Leliana being displeased with you, ending his life won't do anything else.
The Long Road
Trigger: This occurs as a random encounter shortly after Lothering and should happen within the first few trips.
Map: Plains/Highway Road
Description: Caught in an ambush, the player turns the tables and gets the unique chance to have one of the assassins join his cause.
Actions: You meet a traveler on the road who says she was attacked by bandits. She'll ask you to follow her and run off. When you catch up, it becomes clear it was a setup. Kill all the bandits, and you'll find one survivor: their leader, Zevran. You can let him join you as a companion or leave him to die.
Low Road
Trigger: Have the "Darkspawn Ambush!" encounter as above and talk to Wynne back at camp about the ordeal. She will tell you she died in the tower and was revived and now sustained by a good spirit from the Fade that she believes to be a spirit of faith. The next major encounter should be this one.
Map: Plains/Highway Road
Description: In a planned darkspawn ambush, the party is defeated, only to have Wynne revive and bring them back from the brink of death. She discovers the spirit within herself.
Actions: While Wynne is enveloped by the spirit she will be a much more powerful spellcaster. Use her magic against the superior darkspawn numbers. The darkspawn omega is the greatest threat on top of the cliff. Once this is over, she will have unlocked her ability to summon the spirit of faith. Use it as any other talent.