Assuming the character in question wasn't born and raised to be an ninja/ assassin. There are a few cliche ways to get an RP going.
1.The character started as a thief: Great at sticking to the shadows you viewed all possessions as your own, and took what wanted without question. One day you stole from the wrong person(s) and they sent the dark brotherhood after you. After barely surviving you decide to perfect your trade. No mercy and no witnesses.
2. The character was a well rounded warrior, and has a great sense of good and bad. After seeing the horrid conditions of the torture chamber at helgen and the public beheading in solitude; you decided to take justice into your own hands. "You could RP joining the DB or Thieves guild for stealth training, and vow to use those skills to take them down in the future, or use those skills to further their causes."
3.The character is a lone ranger, hardened by the harshness of life. You pick off random bandits quickly and silently. Your name becomes a legend and a whisper, a sellsword of the deadliest caliber. There is no moral good or bad, just a mission to complete and corpses that were in the way. Callousness is the name of this one, you never have to think should I do this or that. If it brings you money it's good. If it doesn't it's irrelevant, and if it's in the way it's dead. IMO the main goal for this one would be working one hold at a time, earn your name or your bounty and do all that is to be done then move on to the next.
Some simple and cliche starts for assassin/rouge/ninja builds. Unfortunatly i'm not all that creative but I hope this helps some XD
Some historical stuff that I've always found super interesting were the reasons behind the actual development of ninjas in feudal Japan, and the skills they trained in. They're definitely not your typical ninja/assassin role-play stories :
From Wikipedia:
"Ninjutsu was developed as a collection of fundamental survivalist techniques in the warring state of feudal Japan. The ninja used their art to ensure their survival in a time of violent political turmoil. Ninjutsu included methods of gathering information, and techniques of non-detection, avoidance, and misdirection. Ninjutsu can also involve training in free running, disguise, escape, concealment, archery, and medicine.[10]
Skills relating to espionage and assassination were highly useful to warring factions in feudal Japan. These persons were literally called "non-humans" (非人 hinin ).[11] At some point the skills of espionage became known collectively as ninjutsu, and the people who specialized in these tasks were called shinobi no mono."
And from the article on Togakure-ryu, supposedly the oldest form of Ninjutsu:
"...it was started in 1162, as a way of fighting in the war between the Genji and Heike (Taira) clans. The style itself would go on to be known as the origination of ninjutsu and its various fighting styles. Nishina was a samurai and a member of the Genji clan, which had been staging a revolt against the Heike clan because of their oppression against the Genji people. The revolt, however, was crushed and Nishina fled his home village of Togakure in Shinano Province to save his children."