The origin of The Illusive Man's eyes is told in the one of the Mass Effect comic books, titled Evolution, the full plot summary of which you can read here on the Mass Effect wikia. It's a 4-issue miniseries, so it's a bit long to completely paste here.
In it, you learn the origins of The Illusive Man and who he was before becoming the leader of Cerberus. I'd highly recommend reading the issues yourself, as it's a nice bit of background information, but I'll write up a quick summary about his eyes.
During the First Contact War, he was part of a mercenary group working for General Williams (Ashley's grandfather). He was exposed to a Prothean relic on Shanxi. Despite the fact that others who were exposed to when it activated ended up basically turning into Husks and losing their higher cognitive abilities, he did not change. However, his eyes were permanently changed and he is able to understand the language that the Husk-like beings now speak. You get to see the more human side of The Illusive Man, what happened to him to engender his pro-humanity stance, and why he believes in it so strongly.
It does not further specify in the comic book series nor in the Mass Effect novels what exactly the impact of this change was, and it is currently part of the mystery of The Illusive Man. The fact that it was a Prothean Relic however, may change your interpretations of his actions and motives.
Tarquin is Lieutenant Tarquin Victus. The Primarchs son.
You rescue him during the mission Tuchanka: Turian Platoon, and afterwards, accompany him on the mission Tuchanka: Bomb.
Sadly, he dies at the end of that last one.
Best Answer
Kai Leng is another character who was originally introduced in the Mass Effect novels, specifically Mass Effect: Retribution and
the one everyone should ignoreMass Effect: Deception.In the books, it's established that he was originally part of the Alliance, but he was imprisoned and dishonorably discharged after committing first-degree murder (killing a krogan with bare hands). He is/was very xenophobic, showing open disgust of other races. That, plus his excellence in combat, drew The Illusive Man's attention. Cerberus broke him out of prison to acquire him as an agent.
He has very strong loyalty to Cerberus and is willing to do whatever The Illusive Man orders him to do, without question. He was initially ordered to hunt down a man named Paul Grayson in order to capture him to do some... questionable experiments on him. Kahlee Sanders, another character originally introduced in the novel, was a friend of Paul Grayson's, and when he contacted her prior to his kidnapping to warn her about Cerberus, she was drawn into a rescue attempt. Kahlee, in turn, is acquainted with David Anderson, who was a Councilor at the time, and enlists his help. He uses his influence help her, motorizing a Turian rescue team to go after Grayson, which ultimately contributes to his removal from the Council.
Though I would be hard-pressed to name a "right hand man" to The Illusive Man, if he had one, Kai Leng would be it. He's pretty much a physical embodiment of the Illusive Man's ideals, pro-human and uncompromising, and The Illusive Man uses Kai Leng's skills accordingly.