In the first two plays in the tetralogy, Richard II and Henry IV Part 1, Shakespeare establishes the idea that England is a ruined garden. In Richard II, the realm is portrayed as a kind of fallen Eden that's been destroyed by King Richard's bad policies (Richard II, 2.1.). In Henry IV Part 1, Hotspur describes how the Percy family helped Henry depose King Richard II when they "put down Richard, that sweet lovely rose, / An plant[ed] this thorn, this canker, Bolingbroke" (1.3.7). By suggesting King Henry IV (formerly called Henry Bolingbroke) is a "thorn" and then a "canker" Hotspur imagines England as a garden that's on the cusp of ruin and decay. (We're noticing a trend here – lousy kings are like lousy gardeners.)
So, we're not surprised when we get to Henry IV Part 2, where the Archbishop of York uses the same analogy to explain why Henry won't punish the rebel leaders:
[…] for full well he knows
He cannot so precisely weed this land
As his misdoubts present occasion:
His foes are so enrooted with his friends
That, plucking to unfix an enemy,
He doth unfasten so and shake a friend. (4.1.10)
In other words, if Henry executes his enemies (the rebel "weeds"), he'll probably end up harming some of his cherished allies as well because political relationships in England are so complicated. (Hmm. Is the Archbishop admitting that his rebellious activity is destroying England?) King Henry says something similar when he complains that Prince Hal's rowdy friends are like "weeds" that have sprung up in rich "soil" as a way of explaining how the unsavory friendships Hal has cultivated are corrupting the young prince (4.4.8).
So, what's up with all the garden imagery? Well, Shakespeare seems interested in conveying just how vulnerable England (and its leaders) can be to corruption and decay. Like a garden, the country must be carefully tended if it's going to flourish. That's just for starters. There's a whole lot more to say about this so go ahead and get your hands dirty.