Perhaps there is a misunderstanding. A member of the crew misinterprets Shepard's actions as being against the greater good. This member then spreads false rumors among the crew, leading them to believe Shepard has betrayed them first, and so they betray him in return. For example, if Shepard made a deal with an alien race that seemed suspect, but in reality it was to save the crew, yet the misinformation led to their betrayal.
One possible story could be that his crew is bribed by a powerful enemy. They turn on him during a crucial mission, leaving Shepard alone to face a difficult situation. Maybe they leak his battle plans or deliberately sabotage his equipment.
In some scenarios, the crew could be under the influence of mind - control. An enemy with advanced technology takes over their minds and forces them to turn against Shepard. Shepard then has to fight not only the external enemy but also his former crewmates while trying to find a way to break the mind - control.
Chapter 528, "Cursed", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event.
Chapter 301, "Stealing Skills", is the clearest early answer because the violence around Until Jiang Li becomes final instead of hypothetical. A useful checkpoint is the way the scene starts with Old Sir Jiang was somewhat puzzled.
Chapter 451, "Where Did This Madwoman Come From?", is the clearest early answer because it turns Yu Li's situation into a concrete plot event. Early on, Upon hearing this, the three people turned their heads in unison..
Chapter 392, "Connected to Shang Shaobai", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event. A useful checkpoint is the way the scene starts with Bai Lu's hopeful heart had sunk once again.
Chapter 529, "Truly a Magical and Complicated Person", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event.
Chapter 547, "What a bustling family you all are", is the clearest early answer because it turns Jiang Yan's situation into a concrete plot event. The chapter turns that into something concrete by moving from Because of the unsightly scandal caused by watching the live...
Chapter 678, "The Biggest Connection in the Circle of Friends!", is the clearest early answer because it turns Jiang's situation into a concrete plot event. Early on, The landlord stood up, maintaining his smile, "Fifty-eight thousand,....
Chapter 370, "Jiang Li, Thank You for Coming to Save Me", is the clearest early answer because it turns Coming's situation into a concrete plot event. Early on, He Yun's trial took place a week later, as scheduled..
Chapter 574, "They Are Ill-fated", is the clearest early answer because it turns Ai Xiaochun's situation into a concrete plot event.
Chapter 888, "You Are Not From This World", is the clearest early answer because it turns Jiang Li's situation into a concrete plot event. The chapter turns that into something concrete by moving from Under the lead of the prison guard, Su Yinwan, for the first time in...