This flower is a hybrid, Bobby. It needs to live in a specific environment or it dies. Some might say it is a bit like us. Well... a bit like some of us. 
Appearing in "Restoration"
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Synopsis for "Restoration"
Logan comes to check in with the X-Men. He walks through a wall... because the wall is not really there, having been destroyed by Juggernaut recently. The X-Men are getting by with hologram technology until they can fix it. Everyone is glad to see Logan.
It turns out he has mail: a package arrived today from Landau, Luckman & Lake. In it, Wolverine finds a wooden box and an advanced device with a button on it. Activating the device, he starts a hologram recording of Zoe Culloden, who regrets she could not deliver the box in person, but due to some problems at the office she needs him to look after it. She warns him that something big and dark is coming, and that the timelines are converging around him. Logan is nonplussed and the X-Men are suspicious, but Logan decides to accept the task.
His first port of call is Sam Guthrie, who has been minding his motorbike. Wolverine admits that Sam did exactly what he asked - take the bike out for a ride every day to break in the engine - but points out that the smoke is a lot darker than it normally is, due to carbon buildup. Sam has been running the bike at a comfortable pace, and motorbikes are designed to go fast.
He also makes a point of talking to Bobby Drake, who is taking a leave from the X-Men to help his dad recover from getting beaten up by racists. The two men admit that time and circumstance have prevented them from being close friends, but Logan says that if he needs help, he only has to ask.
Storm asks the two of them to come up to her greenhouse, where she shows Bobby a plant she grew, a hybrid mutant flower. She cuts it off the plant and gives it to Bobby, as a going-away present.
The X-Men go for a night out to Harry's Hideaway, a Westchester bar they love. However, the night out is getting to Logan: the bar was rebuilt from being wrecked recently, and he regards it as somehow false now. He argues too much with the older X-Men, and he doesn't know the new members. He misses Kurt, Kitty and Jubilee. Eventually, he leaves the bar, and goes to another one, a grimy biker joint called the Auger Inn, whose jukebox is full of musicians who died violently. Drinking alone, Wolverine raises a toast to all the people who suffered from knowing him. At this point, the bartender says he wants to close, and Logan leaves.
Later that night, Logan goes to sit in the abandoned office of Professor X, and proceeds to unburden himself as though his friend were there: his growing feral nature, his sense of isolation. When Logan stops and asks what to do next, the dawn breaks through a nearby window. Logan smiles; now he has his answer.
Putting on his Wolverine costume, Logan goes to the Danger Room and starts up a basic workout routine. But the program goes wrong and spawns a hologram of a tall man in red armor with horns on his head, who informs him that a new age is dawning and he can be a part of it.
Logan responds by stabbing the man in the faceplate, causing part of it to flake off, revealing a skull underneath. With a wave, the man summons a woman in a shroud with a Japanese hairstyle, who Logan recognises as Mariko Yashida, his dead love. The man assures Logan that the power he serves can bring her back to life, that an age of miracles is dawning, and all it will cost him is "one insignificant thing". Logan pauses, then stabs him in the gut. The man cryptically admits that he has known Logan long enough that he should have foreseen this, but that he has time. Mariko wants Logan back, and eventually his guilt at what he is putting her through by seperating them will cause him to relent.
Logan turns to face Mariko, but before he can comfort her, Stick appears, and gently lays her to rest in a nearby mound of earth, saying that she was dragged into the living world, and that eternity is for sleeping. He explains to Logan that the path he's going to choose is the right one, and that the man he just met wants to to pull him off of it. He echoes Zoe Culloden's message, saying that something bad is coming, and says that the path of life will take you into strange lands and away from loved ones, but that this is the path you need to take to grow. Stick pokes the console near the door of the Danger Room, causing himself and the whole scenario to promptly vanish.
Sometime later, Logan packs some stuff and tells the X-Men he is leaving. He has decided to live in the city for a while, to prove he can still be a human. He is taking Zoe Culloden's box, and the bike Sam Guthrie broke in for him. He promises he will come back, but if there's one thing he has decided to prove, it's that Storm was right: he is not a hothouse flower.