It would seem that Bob has been head of the Company for quite some time, and when new possible employees are brought in, he tends to interview them.
Bob first debut was in the first episode of Season 2 "Four Months Later..." He has been following Mohinder Suresh, and listening to his lectures. Later he offers Mohinder membership into the Company, and displays his power of Alchemy/Transmutation by turning a mere metal spoon into a golden one, telling Mohinder that the Company has they're own "Fort Knox" (this is later revealed to be a plan by Mohinder and Mr. Bennet, to infiltrate the Company and destroy from the inside).
He appears in the next episode, "Lizards", and gives Mohinder the mission of curing the Haitian (in Haiti) of the Shanti Virus. He does this and sends the Haitian to Mr. Bennet, claiming to have no memory of what happend.
In "Kindred", Bob shows Mohinder his new lab, Issac Mendez's old loft, something the Company bought after he was killed, and he tells Mohinder that he'll be under constant surveillance, for they're best interests. After leaving, he recieves a call from Niki Sanders, asking if she can be cured. He replies affirmitive, but she has to come in.
In "The Kindness of Strangers", Bob gives Mohinder a taser, and when Niki brakes out of containment and attempts to strangle Bob, Mohinder is forced to use it on her.
In "Fight or Flight", Bob assigns Mohinder a partner, Niki.
In "The Line", Bob tries to get Mohinder to test a new strain of the Shanti Virus on Monica Dawson, without her knowledge. Mohinder doesn't go through with it an throws a chair at the cabinet full of different strains of the Shanti Virus.
Bob's life is threatened in the next episode, "Out of Time" when Maury Parkman is revealed to be working with someone to take down the founding members of the Company. Matt Parkman and Nathan Petrelli come to the Company office, that's being evacuated under Bob's orders, and help Niki, Mohinder and Bob to take down Matt's father. Bob informs Matt that he has his fathers ability, Telepathy, and anything his father can do he can do. Maury uses D.L. to convice Niki that Bob killed him, and she punches Mohinder in the nose, leaving for Bob's office. She breaks down the door by punching it, but Nathan manages to convince Niki out of stabbing Bob with the virus, and she ends up stabbing herself. It is later revealed that Matt trapped his father in Molly's nightmare, and escaped with [[Molly Walker:char:50952], waking her up. The strain of the Shanti Virus that Niki is infected with is revealed to be non-curable by Mohinder's blood. Mohinder later confesses that he's been working with Noah Bennet to take down the Company to Bob. Bob gives Mohinder the answer to curing Niki, Claire Bennet's blood, and with her file, he also hands Mohinder a gun.
We find out in the next episode "Cautionary Tales", that Elle Bishop, is Bob's daughter, and that she's Mohinder's new partner. The three venture to Costa Verde, California, to find Claire. Bob finds her at her school, and later at her home, and kidnappes Claire and ties Sandra to a chair. During this time, West and Mr. Bennet kidnapped Elle, and Bob and Mr. Bennet arrange a swap. During the swap, Claire is flown away by West, but they are shot down by Elle. She is shot in the shoulder by Mr. Bennet, and when Bob runs to her aid, Mr. Bennet approches to shot Bob, but Mr. Bennet is chot by Mohinder first.
The last time we see Bob is in the tenth episode of Season 2, "Truth & Concequences", firstly when he gives the Bennets her "fathers" ashes. After Claire threatens to expose her powers to the world, Bob hopes to calm her by sending Mr. Bennet back to them, revived by Claire's blood. But he is not allowed to stay with them and he has to work for the Company.
More recently, Bob appeared in the online Heroes web-comics. Chapter 67, "The Golden Goose", saw Bob and the Company attempt to track down Richard Drucker, but found his pilot intstead. Bob tortures him by turning his arm into gold, and later turns his whole body into gold. He then appeared in the story arc "The Man With Too Much Brains", but did little more than cameo.
Bob has the power of Alchemy/Transmutation. He is able to change one form of matter into another. Once has he been seen doing this on screen, when he turned a metal spoon into gold. In the web-comics, he has shown the ability to turn a human into gold too, while causing tremendous pain though. Writers ave confirmed that he can change matter into other things than gold though.
It is thought that Bob has to be in conact with an object to transmutate it, as he always has been when he has used his ability.