House and Cuddy are both pretty relationship-averse; they like what they have (or may have given a chance), but neither is especially adept at nurturing it. If it all goes to hell eventually there will be possibly irreparable hurt on both sides.
House understands this, and it is his greatest fear poised on the brink of something new and ultimately terrifying for him. He is able to articulate this fear to Cuddy honestly and painfully in the season premiere “Now What?” He seems caught where he had been in season two ("Need to Know") with Stacy.
But Cuddy reassures House that however screwed up he is, he is one incredible man and he needn't worry about expectations of change. Even though, as House warns, he will likely do "horrible things" to her. It's who he is. But Cuddy is aware of who House; she has fallen in love with House as he is. Why should she want him to change?
There is a tension between the two new lovers beginning right from the second episode "Selfish," now freed of the dreamlike cocoon enfolding them in the premiere. Striking the right balance between their professional—often contentious—relationship, and their strong feelings for each other, has made their dynamic even more complex as both characters try not to dynamite the fledgling affair.
Their efforts not to step on the other’s toes, hence, their reticence to act as they normally would at work nearly costs a patient her life in episode two. It is an important point to address early on, exploring House’s desire not to bend their relationship, refusing to risk it—instead avoiding what he does best: skirting medicine’s conventions and rules.
House is the one always willing to risk himself for the patient; he has never placed much value on his life or welfare. But now something’s changed and the risk is suddenly too great. It’s an important lesson they both must learn if their work and personal relationships have any chance of success. House must practice medicine without regard to Cuddy’s feelings; and court Cuddy as if he were not the maverick rule-breaker he must be to be effective. Cuddy has to be able to reign in her star doctor without fear.
Lying, doing things behind Cuddy’s back, are as much a part of House’s medical practice as his associative leaps. And as much as Cuddy says she doesn’t expect House to change, she wants him to change—at least in some ways. And she's deeply hurt when House does one of those "horrible" things he warns her about in "Now What?"
In the episode (“Office Politics”), House treats the campaign manager during the height of the election season. The only way he believes he can make the diagnosis is by testing the candidate, who House believes has the same condition. Cuddy refuses to allow the test, but House does it anyway—and behind her back, lying about it to her.