I'll try to give an answer that's as intuitive as possible. In probability you can often* replace any statement containing 'or' with addition. If you calculate the probability of throwing 1 or 2 with a dice you get $P(1\ \text{or}\ 2)=P(1\lor2)=P(1)+P(2)=1/6+1/6=1/3$. You can phrase the question 'what is the probability the atom has decayed after 3 half lives?' to 'what is the probability the atom has decayed after 1 half life or after 2 half lives or after three half lives'.
So we can write
$$P(\text{decay in 3 half lives})=\\P(\text{decay during first half life or decay during second half life or decay during third half life})$$
To write this more neatly call $X$ the number of half lives after which the atom decays. Then we get
\begin{align}P(X\leq3)&=P(X=1\ \lor X=2\ \lor X=3)\\
&=P(X=1)+P(X=2)+P(X=3)
\end{align}
The probability of it decaying after one half life is obviously 1/2. To calculate the odds of it decaying during the third half life you have to calculate the probability of it surviving the first half live and surviving the second half life and then decaying during the third half life. I phrased this sentence awkardly on purpose so it is easier to translate into a probability. You can replace 'and' in probability often with multiplication.
\begin{align}P(X=3)=P(&\text{not decay during first half life and}\\
&\text{not decay during second half life}\\&\text{and decay during third half life})\\
=P(&\text{not decay during first half life})\times\\
P(&\text{not decay during second half life})\times\\
P(&\text{decay during third half life})\\
= 1/&2\cdot 1/2 \cdot 1/2=1/8\end{align}
Similarly $P(X=2)=1/2\cdot1/2=1/4$. So finally
$$P(X\leq3)=1/2+1/4+1/8$$
This is the most like your intuive answer, but there is a quicker way. Instead of calculating the probability that it decays in 3 half lives we can calculate the chance of it surviving longer than 3 half lives and invert that probability. Think of the dice again. The chance of not throwing a three is $P(\text{not 3})=1-P(3)$. Similarly $P(X\leq3)=1-P(X>3)=1-(1/2)^3=0.875$. Where $P(X>3)$ is the chance of surviving the first half life and the second and the third.
This answer has become quite long but I hope it's the most clear this way.
*There are cases where this isn't so simple, like in cases with A or B but not both.